libbpp-seq →
2.3.1-8 →
armhf → 2017-08-29 05:34:19
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| libbpp-seq 2.3.1-8 (armhf) Tue, 29 Aug 2017 05:22:29 +0000 |
+==============================================================================+
Package: libbpp-seq
Version: 2.3.1-8
Source Version: 2.3.1-8
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-ab426ba4-d2a4-4845-bf1a-e9dda7a96348' 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 8s (2709 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-seq' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/libbpp-seq.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/libbpp-seq.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 334 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main libbpp-seq 2.3.1-8 (dsc) [2154 B]
Get:2 http://172.17.0.1/private buster-staging/main libbpp-seq 2.3.1-8 (tar) [324 kB]
Get:3 http://172.17.0.1/private buster-staging/main libbpp-seq 2.3.1-8 (diff) [7256 B]
Fetched 334 kB in 0s (761 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/libbpp-seq-2LG6CR/libbpp-seq-2.3.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/libbpp-seq-2LG6CR' 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-yYtiLq/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-yYtiLq/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-yYtiLq/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-yYtiLq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yYtiLq/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yYtiLq/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yYtiLq/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yYtiLq/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (6160 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 29 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-yYtiLq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
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(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-core-dev (>= 2.3.1)
Filtered Build-Depends: debhelper (>= 10), cmake, d-shlibs (>= 0.80), libbpp-core-dev (>= 2.3.1)
dpkg-deb: building package 'sbuild-build-depends-libbpp-seq-dummy' in '/<<BUILDDIR>>/resolver-yYtiLq/apt_archive/sbuild-build-depends-libbpp-seq-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-seq-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-yYtiLq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yYtiLq/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yYtiLq/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yYtiLq/apt_archive ./ Sources [517 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yYtiLq/apt_archive ./ Packages [601 B]
Fetched 2451 B in 0s (6418 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install libbpp-seq 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 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 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-seq-dummy
0 upgraded, 56 newly installed, 0 to remove and 29 not upgraded.
Need to get 27.0 MB of archives.
After this operation, 102 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-yYtiLq/apt_archive ./ sbuild-build-depends-libbpp-seq-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 [601 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 1.24.0-1 [70.4 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 2.3.1-4 [531 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libbpp-core-dev armhf 2.3.1-4 [952 kB]
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
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_2.3.1-4 libbpp-core3_2.3.1-4 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_1.24.0-1 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 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-seq-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 Wed Aug 23 17:45:39 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./libbpp-seq_2.3.1-8.dsc
dpkg-source: info: extracting libbpp-seq in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking libbpp-seq_2.3.1.orig.tar.gz
dpkg-source: info: unpacking libbpp-seq_2.3.1-8.debian.tar.xz
dpkg-source: info: applying unforce-cxxflags.patch
dpkg-source: info: applying rm_VectorProbabilisticSiteContainer.patch
dpkg-source: info: applying relax_test_timeout.patch
Check disk 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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-ab426ba4-d2a4-4845-bf1a-e9dda7a96348
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package libbpp-seq
dpkg-buildpackage: info: source version 2.3.1-8
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build libbpp-seq-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
-- 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-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/depend
make -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-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-seq-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-seq-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target bpp-seq-static
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-static.dir/build
Scanning dependencies of target bpp-seq-shared
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/bpp-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o
[ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o
[ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.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-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp
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-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp
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-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp
[ 1%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:70:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractAlphabet::registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:80:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:94:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& AbstractAlphabet::getState(const std::string& letter) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:103:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t AbstractAlphabet::getStateIndex(const std::string& letter) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:112:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& AbstractAlphabet::getState(int num) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:121:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t AbstractAlphabet::getStateIndex(int num) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& AbstractAlphabet::getState(const std::string& letter) throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:139:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& AbstractAlphabet::getState(int num) throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:148:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& AbstractAlphabet::getStateAt(size_t pos) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:156:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& AbstractAlphabet::getStateAt(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:164:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string AbstractAlphabet::getName(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:171:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string AbstractAlphabet::getName(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:178:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int AbstractAlphabet::charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:185:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string AbstractAlphabet::intToChar(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:212:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> AbstractAlphabet::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:222:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> AbstractAlphabet::getAlias(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:232:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int AbstractAlphabet::getGeneric(const std::vector<int>& states) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:70:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractAlphabet::registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:80:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:258:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string AbstractAlphabet::getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:94:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& AbstractAlphabet::getState(const std::string& letter) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:103:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t AbstractAlphabet::getStateIndex(const std::string& letter) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:112:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& AbstractAlphabet::getState(int num) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:121:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t AbstractAlphabet::getStateIndex(int num) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& AbstractAlphabet::getState(const std::string& letter) throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:139:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& AbstractAlphabet::getState(int num) throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:148:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& AbstractAlphabet::getStateAt(size_t pos) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:156:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& AbstractAlphabet::getStateAt(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:164:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string AbstractAlphabet::getName(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:171:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string AbstractAlphabet::getName(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:178:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int AbstractAlphabet::charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:185:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string AbstractAlphabet::intToChar(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:212:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> AbstractAlphabet::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:222:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> AbstractAlphabet::getAlias(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:232:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int AbstractAlphabet::getGeneric(const std::vector<int>& states) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp:258:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string AbstractAlphabet::getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:89:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool AlphabetTools::checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:104:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool AlphabetTools::checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:111:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:120:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException)
^~~~~
[ 2%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
[ 3%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.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-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp:63:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> BinaryAlphabet::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp:89:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> BinaryAlphabet::getAlias(const std::string& state) const throw (BadCharException)
^~~~~
[ 3%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.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-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp
[ 4%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.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-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp
[ 4%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:108:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getMaskedEquivalentState(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:117:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string getMaskedEquivalentState(const std::string& state) const throw (BadCharException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:83:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:53:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:66:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:78:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int CodonAlphabet::getFirstPosition (int codon) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:85:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int CodonAlphabet::getSecondPosition(int codon) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:92:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int CodonAlphabet::getThirdPosition (int codon) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:100:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:108:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:116:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:89:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool AlphabetTools::checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:104:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool AlphabetTools::checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:111:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.cpp:120:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException)
^~~~~
[ 5%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.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-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:89:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> DNA::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:111:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> DNA::getAlias(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:124:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int DNA::getGeneric(const std::vector<int>& states) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:136:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string DNA::getGeneric(const std::vector<std::string>& states) const throw (BadCharException)
^~~~~
[ 5%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.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-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
[ 6%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.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-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp
[ 7%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/IntegerAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/IntegerAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp:63:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> BinaryAlphabet::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp:89:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> BinaryAlphabet::getAlias(const std::string& state) const throw (BadCharException)
^~~~~
[ 7%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.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-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
[ 8%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.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-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp
[ 8%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.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-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LexicalAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
[ 8%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LexicalAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:108:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getMaskedEquivalentState(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:117:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string getMaskedEquivalentState(const std::string& state) const throw (BadCharException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp:83:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:81:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:82:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:84:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:90:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:91:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:97:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetNumericState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:98:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetNumericState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:115:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double intToValue(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:81:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NumericAlphabet::setState(size_t stateIndex, AlphabetState* st) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:93:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NumericAlphabet::registerState(AlphabetState* st) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:106:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> NumericAlphabet::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:113:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<string> NumericAlphabet::getAlias(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:127:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool NumericAlphabet::containsGap(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:170:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double NumericAlphabet::intToValue(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:181:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetNumericState& NumericAlphabet::getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:186:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetNumericState& NumericAlphabet::getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException)
^~~~~
[ 9%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.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-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:90:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string ProteicAlphabet::getAbbr(const string& aa) const throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:98:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string ProteicAlphabet::getAbbr(int aa) const throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:105:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> ProteicAlphabet::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:135:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<string> ProteicAlphabet::getAlias(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:169:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ProteicAlphabet::getGeneric(const vector<int>& states) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:211:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string ProteicAlphabet::getGeneric(const vector<string>& states) const throw (BadCharException)
^~~~~
[ 9%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.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-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:87:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> RNA::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:109:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> RNA::getAlias(const std::string & state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:122:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int RNA::getGeneric(const std::vector<int> & states) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:134:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string RNA::getGeneric(const std::vector<std::string> & states) const throw (BadCharException)
^~~~~
[ 10%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp
In file included from /usr/include/c++/7/map:60:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:52,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.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 double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, unsigned int>; _KeyOfValue = std::_Select1st<std::pair<const double, unsigned int> >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, unsigned int> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, unsigned int>, std::_Select1st<std::pair<const double, unsigned int> >, std::less<double>, std::allocator<std::pair<const double, unsigned int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, unsigned int> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:52,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:40:
/usr/include/c++/7/bits/stl_map.h: In member function 'virtual void bpp::NumericAlphabet::registerState(bpp::AlphabetState*)':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, unsigned int>, std::_Select1st<std::pair<const double, unsigned int> >, std::less<double>, std::allocator<std::pair<const double, unsigned int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, unsigned int> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h: In member function 'void bpp::NumericAlphabet::remap()':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, unsigned int>, std::_Select1st<std::pair<const double, unsigned int> >, std::less<double>, std::allocator<std::pair<const double, unsigned int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, unsigned int> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h: In member function 'virtual void bpp::NumericAlphabet::setState(size_t, bpp::AlphabetState*)':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, unsigned int>, std::_Select1st<std::pair<const double, unsigned int> >, std::less<double>, std::allocator<std::pair<const double, unsigned int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, unsigned int> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
[ 11%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.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-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:53:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:66:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:78:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int CodonAlphabet::getFirstPosition (int codon) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:85:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int CodonAlphabet::getSecondPosition(int codon) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:92:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int CodonAlphabet::getThirdPosition (int codon) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:100:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:108:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp:116:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:189:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> RNY::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:280:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<string> RNY::getAlias(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:299:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string RNY::getRNY(const string& pos1, const string& pos2, const string& pos3) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:321:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int RNY::getRNY(int i, int j, int k, const Alphabet& alph) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:416:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool RNY::containsGap(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:433:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int RNY::charToInt(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:444:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string RNY::intToChar(int state) const throw (BadIntException)
^~~~~
[ 11%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:89:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> DNA::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:111:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> DNA::getAlias(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:124:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int DNA::getGeneric(const std::vector<int>& states) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.cpp:136:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string DNA::getGeneric(const std::vector<std::string>& states) const throw (BadCharException)
^~~~~
[ 11%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.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-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp
[ 12%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.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-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:160:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool WordAlphabet::containsUnresolved(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:178:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool WordAlphabet::containsGap(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:195:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string WordAlphabet::getName(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:209:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> WordAlphabet::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:233:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> WordAlphabet::getAlias(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:265:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int WordAlphabet::getGeneric(const std::vector<int>& states) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:272:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string WordAlphabet::getGeneric(const std::vector<std::string>& states) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:279:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int WordAlphabet::getWord(const Sequence& seq, size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:296:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int WordAlphabet::getWord(const std::vector<int>& vint, size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:312:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string WordAlphabet::getWord(const std::vector<string>& vpos, size_t pos) const throw (IndexOutOfBoundsException, BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:329:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* WordAlphabet::translate(const Sequence& sequence, size_t pos) const throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:352:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* WordAlphabet::reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:65:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex1Entry(std::istream& input) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:84:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:90:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
[ 12%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.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-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:49:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex1Entry::AAIndex1Entry(std::istream& input) throw (IOException) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:72:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex2Entry(std::istream& input, bool sym = true) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:95:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:102:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:50:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex2Entry::AAIndex2Entry(std::istream& input, bool sym) throw (IOException) :
^~~~~
[ 13%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.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-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp
[ 14%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.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-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
[ 15%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp
[ 15%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.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-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:94:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:95:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:59:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:67:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:98:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:99:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:75:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:102:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:132:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:133:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:65:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:78:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
[ 16%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.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-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
[ 16%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:103:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:104:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/IntegerAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:60:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:69:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/IntegerAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
[ 16%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.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-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp
[ 17%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.h:96:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.h:97:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp:65:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp:73:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
[ 17%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp
[ 18%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.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-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LexicalAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LexicalAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
[ 18%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
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-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:105:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:120:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static GeneticCode* getGeneticCode(const NucleicAlphabet* alphabet, const std::string& description) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:136:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:153:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/EchinodermMitochondrialGeneticCode.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/EchinodermMitochondrialGeneticCode.h:89:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/EchinodermMitochondrialGeneticCode.h:94:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/EchinodermMitochondrialGeneticCode.h:100:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/InvertebrateMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/InvertebrateMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/InvertebrateMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/InvertebrateMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:49:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/StandardGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/StandardGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/StandardGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/StandardGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/VertebrateMitochondrialGeneticCode.h:86:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/VertebrateMitochondrialGeneticCode.h:92:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/VertebrateMitochondrialGeneticCode.h:97:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/VertebrateMitochondrialGeneticCode.h:103:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:51:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/YeastMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/YeastMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/YeastMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/YeastMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:52:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/AscidianMitochondrialGeneticCode.h:86:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/AscidianMitochondrialGeneticCode.h:92:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/AscidianMitochondrialGeneticCode.h:97:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/AscidianMitochondrialGeneticCode.h:103:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:53:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/MoldMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/MoldMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/MoldMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/MoldMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:54:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:54:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:54:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:54:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:54:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceReaderFormat.h:83:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequence* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:55:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOAlignmentReaderFormat.h:82:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IAlignment* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:56:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceWriterFormat.h:82:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OSequence* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:57:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOAlignmentWriterFormat.h:84:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OAlignment* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:58:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOAlphabetIndex1Format.h:107:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex1* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:59:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOAlphabetIndex2Format.h:107:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex2* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:136:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const OrderedSequenceContainer& sequences, const SequenceSelection& selection, SequenceContainer& outputCont) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:155:168: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const SequenceContainer& sequences, const std::vector<std::string>& selection, SequenceContainer& outputCont, bool strict = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:217:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:231:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:252:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:275:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:294:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:158:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:166:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:265:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:321:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:350:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:367:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:418:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:469:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:74:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteSelection getSiteSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:83:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceSelection getSequenceSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:97:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSelectedSites(const SiteContainer& sequences, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:111:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getSelectedSequences(const OrderedSequenceContainer& sequences, const std::string & setName) throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:139:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getPhase(const Comments & maseFileHeader, const std::string &setName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:61:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:61:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:62:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:62:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:62:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:80:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:209:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const string& description) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:234:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:241:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
[ 19%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.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-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
[ 20%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:49:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (SequenceNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
[ 20%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.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-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:81:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:82:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:84:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:90:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:91:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:97:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetNumericState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:98:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetNumericState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:115:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double intToValue(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:81:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NumericAlphabet::setState(size_t stateIndex, AlphabetState* st) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:93:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NumericAlphabet::registerState(AlphabetState* st) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:106:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> NumericAlphabet::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:113:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<string> NumericAlphabet::getAlias(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:127:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool NumericAlphabet::containsGap(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:170:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double NumericAlphabet::intToValue(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:181:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetNumericState& NumericAlphabet::getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:186:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetNumericState& NumericAlphabet::getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:54:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer::AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:107:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& AlignedSequenceContainer::operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:134:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& AlignedSequenceContainer::getSite(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:155:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::setSite(size_t pos, const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:189:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* AlignedSequenceContainer::removeSite(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:219:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::deleteSite(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:242:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:270:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSite(const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:307:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSite(const Site& site, int position, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:343:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSite(const Site& site, size_t siteIndex, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:383:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSite(const Site& site, size_t siteIndex, int position, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:433:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::setSequence(size_t i, const Sequence& sequence, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:448:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::setSequence(const string& name, const Sequence& sequence, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:461:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSequence(const Sequence& sequence, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:478:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSequence(const Sequence& sequence, size_t i, bool checkName) throw (Exception)
^~~~~
In file included from /usr/include/c++/7/map:60:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.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<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:60:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:52,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.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 double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, unsigned int>; _KeyOfValue = std::_Select1st<std::pair<const double, unsigned int> >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, unsigned int> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, unsigned int>, std::_Select1st<std::pair<const double, unsigned int> >, std::less<double>, std::allocator<std::pair<const double, unsigned int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, unsigned int> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:52,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp:40:
/usr/include/c++/7/bits/stl_map.h: In member function 'virtual void bpp::NumericAlphabet::registerState(bpp::AlphabetState*)':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, unsigned int>, std::_Select1st<std::pair<const double, unsigned int> >, std::less<double>, std::allocator<std::pair<const double, unsigned int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, unsigned int> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
In file included from /usr/include/c++/7/map:61:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/usr/include/c++/7/bits/stl_map.h: In static member function 'static bpp::Site* bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(const bpp::Site&, const bpp::GeneticCode&, double)':
/usr/include/c++/7/bits/stl_map.h:512:4: 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:512:4: 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:512:4: 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: In member function 'void bpp::NumericAlphabet::remap()':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, unsigned int>, std::_Select1st<std::pair<const double, unsigned int> >, std::less<double>, std::allocator<std::pair<const double, unsigned int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, unsigned int> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h: In member function 'virtual void bpp::NumericAlphabet::setState(size_t, bpp::AlphabetState*)':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, unsigned int>, std::_Select1st<std::pair<const double, unsigned int> >, std::less<double>, std::allocator<std::pair<const double, unsigned int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, unsigned int> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
[ 21%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp
[ 22%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.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-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:90:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string ProteicAlphabet::getAbbr(const string& aa) const throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:98:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string ProteicAlphabet::getAbbr(int aa) const throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:105:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> ProteicAlphabet::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:135:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<string> ProteicAlphabet::getAlias(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:169:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ProteicAlphabet::getGeneric(const vector<int>& states) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp:211:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string ProteicAlphabet::getGeneric(const vector<string>& states) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:97:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
CompressedVectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:142:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:143:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:144:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:145:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:146:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:147:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:148:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = false) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:152:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:153:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = false) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:169:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:172:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:173:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:178:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:198:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:208:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:214:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:219:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:233:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:239:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:255:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:261:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:267:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:273:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:54:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& CompressedVectorSiteContainer::getSite(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:239:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::setSite(size_t pos, const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:316:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* CompressedVectorSiteContainer::removeSite(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:327:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:358:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:368:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::addSite(const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:391:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::addSite(const Site& site, size_t siteIndex, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:440:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& CompressedVectorSiteContainer::getSequence(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:458:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& CompressedVectorSiteContainer::getSequence(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:478:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t CompressedVectorSiteContainer::getSequencePosition(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:535:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:559:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException)
^~~~~
[ 22%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.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-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp
[ 23%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.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-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:87:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequenceByKey(const std::string& key) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:97:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequenceByKey(const std::string& key , const Sequence& sequence, bool checkNames = true) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:106:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequenceByKey(const std::string& key) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:114:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequenceByKey(const std::string& key) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const std::string& key, const Sequence& sequence, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:135:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getKey(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:142:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getKey(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:159:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:166:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkNames = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:170:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:171:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:172:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:177:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:181:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:194:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:217:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:218:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:219:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:220:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:221:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:224:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:232:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:233:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& MapSequenceContainer::getSequence(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:108:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& MapSequenceContainer::getSequence(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:130:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& MapSequenceContainer::getSequence_(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:141:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& MapSequenceContainer::getSequence_(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:153:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:164:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:180:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:209:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::setSequence(const string& name, const Sequence& sequence, bool checkNames) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:237:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::setSequenceByKey(const string& key, const Sequence& sequence, bool checkNames) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:265:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* MapSequenceContainer::removeSequence(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:278:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* MapSequenceContainer::removeSequence(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:293:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* MapSequenceContainer::removeSequenceByKey(const string& key)throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:306:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::deleteSequence(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:318:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::deleteSequence(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::deleteSequenceByKey(const string& key) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:344:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::addSequence(const string& key, const Sequence& sequence, bool checkNames) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:380:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string MapSequenceContainer::getKey(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:391:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string MapSequenceContainer::getKey(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:405:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::setComments(size_t pos, const Comments& comments) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:426:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::setSequencesNames(const vector<string>& names, bool checkNames) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceIterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:194:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:258:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:285:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:312:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:343:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:366:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:393:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:420:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:451:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:487:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:537:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:554:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:568:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQualities(const std::vector<int>& quality) throw (DimensionException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:599:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:623:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:647:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:660:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:676:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:683:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:702:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:709:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:723:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:730:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:747:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
[ 24%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.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-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:136:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const OrderedSequenceContainer& sequences, const SequenceSelection& selection, SequenceContainer& outputCont) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:155:168: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const SequenceContainer& sequences, const std::vector<std::string>& selection, SequenceContainer& outputCont, bool strict = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:217:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:231:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:252:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:275:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:294:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:71:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceContainer& outputCont) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:97:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceContainer& outputCont, bool strict) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:204:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceContainer* SequenceContainerTools::getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException)
^~~~~
[ 24%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.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-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerExceptions.cpp
In file included from /usr/include/c++/7/map:60:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.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 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 /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/usr/include/c++/7/bits/stl_map.h: In static member function 'static void bpp::SequenceContainerTools::getFrequencies(const bpp::SequenceContainer&, std::map<int, double>&, 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,
^~~
[ 25%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.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-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp
[ 25%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.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-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp
[ 26%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.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-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:52:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:158:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& VectorSequenceContainer::getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:181:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& VectorSequenceContainer::getSequence(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:194:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& VectorSequenceContainer::getSequence_(size_t sequenceIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:204:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& VectorSequenceContainer::getSequence_(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:217:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t VectorSequenceContainer::getSequencePosition(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:230:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSequenceContainer::setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:258:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* VectorSequenceContainer::removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:272:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSequenceContainer::deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:284:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSequenceContainer::addSequence(const Sequence& sequence, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:307:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSequenceContainer::addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:347:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:384:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSequenceContainer::setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException)
^~~~~
[ 26%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:158:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:166:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:265:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:321:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:350:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:367:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:418:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:469:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:136:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const OrderedSequenceContainer& sequences, const SequenceSelection& selection, SequenceContainer& outputCont) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:155:168: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const SequenceContainer& sequences, const std::vector<std::string>& selection, SequenceContainer& outputCont, bool strict = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:217:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:231:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:252:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:275:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:294:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:341:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SiteContainer* SiteContainerTools::removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:360:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SiteContainerTools::removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:377:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:480:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:579:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:680:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:841:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double SiteContainerTools::computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist, const std::string& gapOption, bool unresolvedAsGap) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:940:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:87:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> RNA::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:109:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> RNA::getAlias(const std::string & state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:122:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int RNA::getGeneric(const std::vector<int> & states) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.cpp:134:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string RNA::getGeneric(const std::vector<std::string> & states) const throw (BadCharException)
^~~~~
[ 26%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.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-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:56:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:290:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& VectorSiteContainer::getSite(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:299:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::setSite(size_t pos, const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:329:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* VectorSiteContainer::removeSite(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:340:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::deleteSite(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:350:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:363:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::addSite(const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:392:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::addSite(const Site& site, int position, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:421:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::addSite(const Site& site, size_t siteIndex, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:454:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::addSite(const Site& site, size_t siteIndex, int position, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:529:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& VectorSiteContainer::getSequence(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:549:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& VectorSiteContainer::getSequence(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:571:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t VectorSiteContainer::getSequencePosition(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:584:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::setSequence(const string& name, const Sequence& sequence, bool checkNames) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:594:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:637:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* VectorSiteContainer::removeSequence(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:663:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* VectorSiteContainer::removeSequence(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:672:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::deleteSequence(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:693:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::deleteSequence(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:702:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::addSequence(const Sequence& sequence, bool checkNames) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:746:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:835:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:859:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException)
^~~~~
[ 27%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.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-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:82:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:83:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:84:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:88:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:89:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:90:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:47:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int DNAToRNA::translate(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:55:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string DNAToRNA::translate(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:63:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int DNAToRNA::reverse(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:71:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string DNAToRNA::reverse(const std::string& state) const throw (BadCharException)
^~~~~
[ 27%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.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-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.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/VectorTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.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<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/VectorTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/usr/include/c++/7/bits/stl_map.h: In static member function 'static bpp::SiteContainer* bpp::SiteContainerTools::removeGapSites(const bpp::SiteContainer&, double)':
/usr/include/c++/7/bits/stl_map.h:512:4: 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,
^~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.cpp:45:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t DistanceMatrix::getNameIndex(const std::string& name) const throw (Exception)
^~~~~
/usr/include/c++/7/bits/stl_map.h: In static member function 'static void bpp::SiteContainerTools::removeGapSites(bpp::SiteContainer&, double)':
/usr/include/c++/7/bits/stl_map.h:512:4: 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,
^~~
[ 28%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp
[ 29%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.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-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
[ 29%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
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-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:86:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:92:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:97:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:103:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:189:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> RNY::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:280:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<string> RNY::getAlias(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:299:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string RNY::getRNY(const string& pos1, const string& pos2, const string& pos3) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:321:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int RNY::getRNY(int i, int j, int k, const Alphabet& alph) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:416:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool RNY::containsGap(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:433:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int RNY::charToInt(const string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.cpp:444:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string RNY::intToChar(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
[ 30%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.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-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:89:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:94:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:100:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
[ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:160:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool WordAlphabet::containsUnresolved(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:178:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool WordAlphabet::containsGap(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:195:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string WordAlphabet::getName(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:209:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> WordAlphabet::getAlias(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:233:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> WordAlphabet::getAlias(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:265:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int WordAlphabet::getGeneric(const std::vector<int>& states) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:272:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string WordAlphabet::getGeneric(const std::vector<std::string>& states) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:279:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int WordAlphabet::getWord(const Sequence& seq, size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:296:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int WordAlphabet::getWord(const std::vector<int>& vint, size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:312:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string WordAlphabet::getWord(const std::vector<string>& vpos, size_t pos) const throw (IndexOutOfBoundsException, BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:329:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* WordAlphabet::translate(const Sequence& sequence, size_t pos) const throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.cpp:352:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* WordAlphabet::reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
^~~~~
[ 31%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.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-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp
[ 31%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.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-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
[ 32%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.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-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
[ 33%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:65:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex1Entry(std::istream& input) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:84:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h:90:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp:49:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex1Entry::AAIndex1Entry(std::istream& input) throw (IOException) :
^~~~~
[ 33%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.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-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
[ 34%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.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-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:86:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:92:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:97:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:103:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
[ 34%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.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-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
[ 34%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:72:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex2Entry(std::istream& input, bool sym = true) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:95:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h:102:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:82:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IAlignment* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:111:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:122:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:125:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:136:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:143:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:144:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:184:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:185:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:186:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:75:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:89:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:103:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:113:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:114:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:76:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:87:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:101:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:112:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:115:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:144:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence_(const std::string & s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:56:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IAlignment* BppOAlignmentReaderFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp:50:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex2Entry::AAIndex2Entry(std::istream& input, bool sym) throw (IOException) :
^~~~~
[ 35%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp
[ 36%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.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-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp
[ 36%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
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-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:94:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h:95:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
[ 37%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.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-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:59:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp:67:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AlphabetIndex1.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h:107:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex1* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:84:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OAlignment* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:75:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:89:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:103:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:113:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:114:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:111:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:122:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:125:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:136:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:143:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:144:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:184:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:185:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:186:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:83:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:84:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:55:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OAlignment* BppOAlignmentWriterFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAPolarityIndex.h:106:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAPolarityIndex.h:112:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAVolumeIndex.h:109:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAVolumeIndex.h:115:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/KleinAANetChargeIndex.h:106:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/KleinAANetChargeIndex.h:112:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanAHelixIndex.h:92:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanAHelixIndex.h:98:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanBSheetIndex.h:92:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanBSheetIndex.h:98:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanTurnIndex.h:92:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanTurnIndex.h:98:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h:104:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h:110:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:49:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASurfaceIndex.h:90:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:49:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASurfaceIndex.h:96:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAMassIndex.h:90:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAMassIndex.h:96:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:51:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAVolumeIndex.h:92:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:51:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAVolumeIndex.h:98:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:52:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChargeIndex.h:133:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:52:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChargeIndex.h:139:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:53:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEAInf10Index.h:90:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEAInf10Index.h:96:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:54:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEA1030Index.h:90:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEA1030Index.h:96:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:55:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEASup30Index.h:90:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEASup30Index.h:96:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:56:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex1Entry.h:65:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex1Entry(std::istream& input) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex1Entry.h:84:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex1Entry.h:90:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:67:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex1* BppOAlphabetIndex1Format::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.h:107:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex2* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h:107:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex1* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/BLOSUM50.h:94:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/BLOSUM50.h:95:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAChemicalDistance.h:132:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAChemicalDistance.h:133:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/MiyataAAChemicalDistance.h:103:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/MiyataAAChemicalDistance.h:104:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/SimpleIndexDistance.h:89:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/SimpleIndexDistance.h:95:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex2Entry.h:72:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex2Entry(std::istream& input, bool sym = true) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex2Entry.h:95:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex2Entry.h:102:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:59:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex2* BppOAlphabetIndex2Format::read(const std::string& description) throw (Exception)
^~~~~
[ 37%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.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-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
[ 38%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.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-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp
[ 38%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:83:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequence* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:111:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:122:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:125:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:136:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:143:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:144:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:184:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:185:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:186:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:75:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:89:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:103:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:113:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:114:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:76:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:87:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:75:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:101:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:112:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:115:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:144:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence_(const std::string & s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:57:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequence* BppOSequenceReaderFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
[ 39%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
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-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:81:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequenceStream* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:98:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h:99:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:75:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp:102:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:51:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequenceStream* BppOSequenceStreamReaderFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:82:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OSequence* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:52:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OSequence* BppOSequenceWriterFormat::read(const std::string& description) throw (Exception)
^~~~~
[ 39%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.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-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp
[ 40%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
[ 41%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.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-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:132:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h:133:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:75:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:89:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:103:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:113:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:114:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:52:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Clustal::appendAlignmentFromStream(std::istream& input, SiteContainer & sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:114:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Clustal::writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:65:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp:78:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
[ 41%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.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-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:76:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:87:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:52:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DCSE::appendAlignmentFromStream(istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:56:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool Fasta::nextSequence(istream& input, Sequence& seq) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:116:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::writeSequence(ostream& output, const Sequence& seq) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:147:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::appendSequencesFromStream(istream& input, SequenceContainer& vsc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:204:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::writeSequences(ostream& output, const SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:231:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::FileIndex::build(const std::string& path, const bool strictSequenceNames) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:255:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
streampos Fasta::FileIndex::getSequencePosition(const std::string& id) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:263:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::FileIndex::read(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:277:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::FileIndex::write(const std::string& path) throw (Exception) {
^~~~~
[ 42%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.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-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp
[ 42%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.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-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:75:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:50:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void GenBank::appendSequencesFromStream(std::istream& input, SequenceContainer& vsc) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:75:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:89:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:103:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:113:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:114:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:76:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:87:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:111:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:122:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:125:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:136:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:143:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:144:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:184:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:185:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:186:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:75:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:101:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:112:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:115:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:144:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence_(const std::string & s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:63:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequence* IoSequenceFactory::createReader(const string& format) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:78:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IAlignment* IoSequenceFactory::createAlignmentReader(const string& format) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:92:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OSequence* IoSequenceFactory::createWriter(const string& format) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:99:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OAlignment* IoSequenceFactory::createAlignmentWriter(const string& format) throw (Exception)
^~~~~
[ 43%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.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-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp
[ 43%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.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-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp
[ 44%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.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-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:136:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const OrderedSequenceContainer& sequences, const SequenceSelection& selection, SequenceContainer& outputCont) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:155:168: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const SequenceContainer& sequences, const std::vector<std::string>& selection, SequenceContainer& outputCont, bool strict = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:217:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:231:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:252:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:275:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:294:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:49:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Mase::appendSequencesFromStream(std::istream& input, SequenceContainer& vsc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:119:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Mase::writeSequences(ostream& output, const SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Mase::readHeader_(std::istream& input, MaseHeader& header) const throw (Exception)
^~~~~
[ 44%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:158:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:166:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:265:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:321:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:350:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:367:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:418:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:469:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:74:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteSelection getSiteSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:83:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceSelection getSequenceSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:97:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSelectedSites(const SiteContainer& sequences, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:111:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getSelectedSequences(const OrderedSequenceContainer& sequences, const std::string & setName) throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:139:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getPhase(const Comments & maseFileHeader, const std::string &setName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:52:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SiteSelection MaseTools::getSiteSet(const Comments& maseFileHeader, const string& setName) throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:104:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceSelection MaseTools::getSequenceSet(const Comments& maseFileHeader, const string& setName) throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:153:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const string& setName) throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:163:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& setName) throw (IOException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:246:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t MaseTools::getPhase(const Comments& maseFileHeader, const string& setName) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:101:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:112:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:115:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:144:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence_(const std::string & s) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusTools.h:77:117: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool getNextCommand(std::istream& input, std::string& name, std::string& arguments, bool lineBrk = true) throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:158:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:166:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:265:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:321:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:350:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:367:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:418:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:469:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:57:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> NexusIOSequence::splitNameAndSequence_(const std::string& s) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:70:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOSequence::appendAlignmentFromStream(std::istream& input, SiteContainer& vsc) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:103:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h:104:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:60:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp:69:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
[ 44%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.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-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusTools.h:77:117: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool getNextCommand(std::istream& input, std::string& name, std::string& arguments, bool lineBrk = true) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusTools.cpp:73:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException)
^~~~~
[ 45%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.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-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp
[ 45%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.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-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
[ 46%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.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-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp
[ 47%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:74:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:194:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:258:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:285:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:312:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:343:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:366:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:393:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:420:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:451:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:487:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:537:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:554:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:568:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQualities(const std::vector<int>& quality) throw (DimensionException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:599:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:623:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:647:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:660:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:676:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:683:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:702:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:709:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:723:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:730:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:747:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:97:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:116:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:52:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool PhredPhd::nextSequence(std::istream& input, Sequence& seq) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:59:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool PhredPhd::nextSequence(std::istream& input, Sequence& seq, std::vector<int>& pos) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:54:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool PhredPoly::nextSequence(istream& input, Sequence& seq) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.h:96:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.h:97:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp:65:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp:73:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:111:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:122:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:125:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:136:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:143:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:144:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:184:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:185:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:186:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:136:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const OrderedSequenceContainer& sequences, const SequenceSelection& selection, SequenceContainer& outputCont) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:155:168: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const SequenceContainer& sequences, const std::vector<std::string>& selection, SequenceContainer& outputCont, bool strict = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:217:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:231:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:252:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:275:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:294:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:55:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> Phylip::splitNameAndSequence(const std::string& s) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Phylip::readSequential(std::istream& in, SiteContainer& asc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:132:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Phylip::readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:174:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Phylip::appendAlignmentFromStream(std::istream& input, SiteContainer& vsc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:185:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int Phylip::getNumberOfSequences(const std::string& path) const throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:279:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Phylip::writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
[ 48%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp
[ 49%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.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-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp
[ 49%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.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-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:83:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:84:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:54:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Stockholm::writeAlignment(ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:105:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:120:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static GeneticCode* getGeneticCode(const NucleicAlphabet* alphabet, const std::string& description) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:136:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.h:153:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/EchinodermMitochondrialGeneticCode.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/EchinodermMitochondrialGeneticCode.h:89:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/EchinodermMitochondrialGeneticCode.h:94:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/EchinodermMitochondrialGeneticCode.h:100:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/InvertebrateMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/InvertebrateMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/InvertebrateMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/InvertebrateMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:49:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/StandardGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/StandardGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/StandardGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/StandardGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/VertebrateMitochondrialGeneticCode.h:86:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/VertebrateMitochondrialGeneticCode.h:92:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/VertebrateMitochondrialGeneticCode.h:97:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/VertebrateMitochondrialGeneticCode.h:103:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:51:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/YeastMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/YeastMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/YeastMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/YeastMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:52:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/AscidianMitochondrialGeneticCode.h:86:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/AscidianMitochondrialGeneticCode.h:92:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/AscidianMitochondrialGeneticCode.h:97:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/AscidianMitochondrialGeneticCode.h:103:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:53:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/MoldMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/MoldMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/MoldMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../GeneticCode/MoldMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:54:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:54:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:54:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:54:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:54:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceReaderFormat.h:83:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequence* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:55:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOAlignmentReaderFormat.h:82:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IAlignment* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:56:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOSequenceWriterFormat.h:82:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OSequence* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:57:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOAlignmentWriterFormat.h:84:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OAlignment* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:58:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOAlphabetIndex1Format.h:107:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex1* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:59:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/BppOAlphabetIndex2Format.h:107:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex2* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:136:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const OrderedSequenceContainer& sequences, const SequenceSelection& selection, SequenceContainer& outputCont) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:155:168: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const SequenceContainer& sequences, const std::vector<std::string>& selection, SequenceContainer& outputCont, bool strict = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:217:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:231:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:252:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:275:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SequenceContainerTools.h:294:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/../DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:158:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:166:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:265:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:321:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:350:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:367:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:418:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/../Container/SiteContainerTools.h:469:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:74:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteSelection getSiteSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:83:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceSelection getSequenceSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:97:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSelectedSites(const SiteContainer& sequences, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:111:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getSelectedSequences(const OrderedSequenceContainer& sequences, const std::string & setName) throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:60:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../Io/MaseTools.h:139:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getPhase(const Comments & maseFileHeader, const std::string &setName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:61:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:61:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:62:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:62:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:62:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/../SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:80:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:209:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const string& description) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:234:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/App/SequenceApplicationTools.cpp:241:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:194:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:258:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:285:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:312:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:343:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:366:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:393:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:420:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:451:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:487:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:537:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:554:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:568:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQualities(const std::vector<int>& quality) throw (DimensionException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:599:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:623:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:647:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:660:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:676:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:683:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:702:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:709:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:723:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:730:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:747:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
[ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.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-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
[ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
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-seq-static.dir/Bpp/Seq/Sequence.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:70:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int NucleicAcidsReplication::translate(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:76:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string NucleicAcidsReplication::translate(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:82:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* NucleicAcidsReplication::translate(const Sequence& sequence) const throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:96:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int NucleicAcidsReplication::reverse(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:102:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string NucleicAcidsReplication::reverse(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:108:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* NucleicAcidsReplication::reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:65:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:78:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:90:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:100:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:109:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:119:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:156:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSequence::setContent(const std::string& sequence) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:205:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSequence::append(const Sequence& seq) throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:214:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSequence::append(const std::vector<int>& content) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:225:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSequence::append(const std::vector<std::string>& content) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:237:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSequence::append(const std::string& content) throw (BadCharException)
^~~~~
[ 51%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.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-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
[ 51%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.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-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.cpp
[ 52%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.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-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
[ 52%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp
[ 52%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.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-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:81:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getAlignmentPosition(size_t seqPos) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:82:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(size_t alnPos) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:49:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t SequenceWalker::getAlignmentPosition(size_t seqPos) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:81:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t SequenceWalker::getSequencePosition(size_t alnPos) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:88:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::concatenate(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:108:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& SequenceTools::complement(Sequence& seq) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:133:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::getComplement(const Sequence& sequence) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:155:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::transcript(const Sequence& sequence) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:168:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::reverseTranscript(const Sequence& sequence) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:245:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double SequenceTools::getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps) throw (AlphabetMismatchException, SequenceNotAlignedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:365:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:383:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceTools::removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:397:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceTools::replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:413:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (SequenceNotAlignedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:518:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:543:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::subtractHaplotype(const Sequence& s, const Sequence& h, string name, unsigned int level) throw (SequenceNotAlignedException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:577:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::RNYslice(const Sequence& seq, int ph) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:619:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::RNYslice(const Sequence& seq) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
[ 53%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.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-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
[ 54%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:62:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:72:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:82:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:89:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:96:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:103:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:143:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceWithAnnotation::setContent(const std::string& sequence) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:206:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceWithAnnotation::append(const Sequence& seq) throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:218:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceWithAnnotation::append(const std::vector<int>& content) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:233:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceWithAnnotation::append(const std::vector<std::string>& content) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:249:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceWithAnnotation::append(const std::string& content) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:270:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:49:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (SequenceNotFoundException)
^~~~~
[ 54%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /usr/include/c++/7/map:60:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.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<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 /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/CodonSiteTools.cpp:40:
/usr/include/c++/7/bits/stl_map.h: In static member function 'static bpp::Site* bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(const bpp::Site&, const bpp::GeneticCode&, double)':
/usr/include/c++/7/bits/stl_map.h:512:4: 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:512:4: 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:512:4: 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,
^~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:54:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer::AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:107:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& AlignedSequenceContainer::operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:134:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& AlignedSequenceContainer::getSite(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:155:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::setSite(size_t pos, const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:189:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* AlignedSequenceContainer::removeSite(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:219:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::deleteSite(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:242:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:270:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSite(const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:307:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSite(const Site& site, int position, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:343:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSite(const Site& site, size_t siteIndex, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:383:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSite(const Site& site, size_t siteIndex, int position, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:433:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::setSequence(size_t i, const Sequence& sequence, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:448:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::setSequence(const string& name, const Sequence& sequence, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:461:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSequence(const Sequence& sequence, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:478:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AlignedSequenceContainer::addSequence(const Sequence& sequence, size_t i, bool checkName) throw (Exception)
^~~~~
[ 54%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.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-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp
[ 55%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:97:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
CompressedVectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:142:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:143:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:144:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:145:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:146:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:147:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:148:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = false) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:152:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:153:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = false) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:169:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:172:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:173:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:178:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:198:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:208:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:214:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:219:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:233:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:239:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:255:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:261:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:267:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:273:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception, NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:54:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& CompressedVectorSiteContainer::getSite(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:239:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::setSite(size_t pos, const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:316:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* CompressedVectorSiteContainer::removeSite(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:327:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:174:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:358:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:368:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::addSite(const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:391:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::addSite(const Site& site, size_t siteIndex, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:440:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& CompressedVectorSiteContainer::getSequence(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:458:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& CompressedVectorSiteContainer::getSequence(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:478:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t CompressedVectorSiteContainer::getSequencePosition(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:535:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation* createMaskAnnotation(const Sequence& seq) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:108:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getMaskedEquivalentState(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:559:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CompressedVectorSiteContainer::setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:117:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string getMaskedEquivalentState(const std::string& state) const throw (BadCharException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:74:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation* SequenceWithAnnotationTools::createMaskAnnotation(const Sequence& seq) throw (AlphabetException)
^~~~~
[ 56%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.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-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:194:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:258:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:285:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:312:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:343:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:366:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:393:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:420:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:451:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:487:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:537:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:554:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:568:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQualities(const std::vector<int>& quality) throw (DimensionException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:599:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:623:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:647:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:660:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:676:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:683:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:702:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:709:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:723:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:730:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:747:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
[ 57%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.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-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp
[ 57%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.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-seq-static.dir/Bpp/Seq/Site.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
[ 58%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.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-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteExceptions.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:58:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site::Site(const vector<string>& site, const Alphabet* alpha) throw (BadCharException) : AbstractCoreSite(), BasicSymbolList(site, alpha) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:60:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site::Site(const vector<string>& site, const Alphabet* alpha, int position) throw (BadCharException) : AbstractCoreSite(position), BasicSymbolList(site, alpha) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:62:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site::Site(const vector<int>& site, const Alphabet* alpha) throw (BadIntException) : AbstractCoreSite(), BasicSymbolList(site, alpha) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:64:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site::Site(const vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException) : AbstractCoreSite(position), BasicSymbolList(site, alpha) {}
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:194:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:258:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:285:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:312:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:343:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:366:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:393:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:420:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:451:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:487:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:537:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:554:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:568:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQualities(const std::vector<int>& quality) throw (DimensionException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:599:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:623:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:647:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:660:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:676:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:683:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:702:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:709:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:723:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:730:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:747:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:77:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const SequenceWithQuality& sequence, size_t begin, size_t end, SequenceWithQuality& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:97:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceWithQuality* subseq(const SequenceWithQuality& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:122:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetMismatchException, Exception) ;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:135:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:148:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:162:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:54:130: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithQuality* SequenceWithQualityTools::concatenate(const SequenceWithQuality& seqwq1, const SequenceWithQuality& seqwq2) throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:77:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithQuality* SequenceWithQualityTools::complement(const SequenceWithQuality& sequence) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:101:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithQuality* SequenceWithQualityTools::transcript(const SequenceWithQuality& sequence) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:116:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithQuality* SequenceWithQualityTools::reverseTranscript(const SequenceWithQuality& sequence) throw (AlphabetException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteExceptions.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteExceptions.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteExceptions.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
[ 58%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.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-seq-static.dir/Bpp/Seq/SiteTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp
[ 58%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:87:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequenceByKey(const std::string& key) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:97:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequenceByKey(const std::string& key , const Sequence& sequence, bool checkNames = true) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:106:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequenceByKey(const std::string& key) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:114:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequenceByKey(const std::string& key) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const std::string& key, const Sequence& sequence, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:135:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getKey(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:142:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getKey(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:159:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:166:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkNames = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:170:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:171:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:172:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:177:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:181:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:194:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:217:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:218:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:219:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:220:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:221:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:224:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:232:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.h:233:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& MapSequenceContainer::getSequence(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:108:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& MapSequenceContainer::getSequence(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:130:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& MapSequenceContainer::getSequence_(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:141:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& MapSequenceContainer::getSequence_(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:153:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:164:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:180:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:209:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::setSequence(const string& name, const Sequence& sequence, bool checkNames) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:237:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::setSequenceByKey(const string& key, const Sequence& sequence, bool checkNames) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:265:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* MapSequenceContainer::removeSequence(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:278:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* MapSequenceContainer::removeSequence(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:293:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* MapSequenceContainer::removeSequenceByKey(const string& key)throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:306:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::deleteSequence(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:318:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::deleteSequence(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::deleteSequenceByKey(const string& key) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:344:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::addSequence(const string& key, const Sequence& sequence, bool checkNames) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:380:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string MapSequenceContainer::getKey(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:391:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string MapSequenceContainer::getKey(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:405:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::setComments(size_t pos, const Comments& comments) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/MapSequenceContainer.cpp:426:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MapSequenceContainer::setSequencesNames(const vector<string>& names, bool checkNames) throw (Exception)
^~~~~
[ 59%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.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-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.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 /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static double bpp::SiteTools::heterozygosity(const bpp::Site&)':
/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/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/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/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:61:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string StringSequenceTools::subseq(const string& sequence, size_t begin, size_t end) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:194:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double StringSequenceTools::getGCcontent(const string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:273:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:290:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string StringSequenceTools::decodeSequence(const vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:303:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (EmptySequenceException, SequenceException, AlphabetException)
^~~~~
[ 59%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.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-seq-static.dir/Bpp/Seq/SymbolList.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:49:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList::BasicSymbolList(const std::vector<string>& list, const Alphabet* alpha) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:55:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList::BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:91:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::setContent(const vector<string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:107:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::setContent(const vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:127:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::addElement(const string& c) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:134:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::addElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:142:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::setElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string BasicSymbolList::getChar(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:169:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::deleteElement(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:178:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:187:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::addElement(int v) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:196:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:207:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:218:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int BasicSymbolList::getValue(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:230:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList::EdSymbolList(const std::vector<string>& list, const Alphabet* alpha) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:236:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList::EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:291:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::setContent(const vector<string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:311:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::setContent(const vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:335:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::addElement(const string& c) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:345:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::addElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:356:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::setElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:368:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string EdSymbolList::getChar(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:383:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::deleteElement(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:395:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:408:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::addElement(int v) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:420:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:434:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:448:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int EdSymbolList::getValue(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
[ 60%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.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-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp
[ 61%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
[ 61%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.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-seq-static.dir/Bpp/Seq/Transliterator.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:69:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SymbolListTools::getCounts(const SymbolList& list1, const SymbolList& list2, map< int, map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:103:152: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SymbolListTools::getFrequencies(const SymbolList& list1, const SymbolList& list2, map<int, map<int, double> >& frequencies, bool resolveUnknowns) throw (DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:115:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double SymbolListTools::getGCContent(const SymbolList& list, bool ignoreUnresolved, bool ignoreGap) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:154:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t SymbolListTools::getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:165:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t SymbolListTools::getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceIterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:194:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:258:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:285:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:312:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:343:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:366:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:393:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:420:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:451:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:487:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:537:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:554:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:568:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQualities(const std::vector<int>& quality) throw (DimensionException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:599:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:623:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:647:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:660:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:676:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:683:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:702:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:709:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:723:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:730:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceWithQuality.h:747:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
[ 61%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp
[ 62%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerExceptions.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /usr/include/c++/7/map:60:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.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 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/Seq/Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /usr/include/c++/7/map:61:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:40:
/usr/include/c++/7/bits/stl_map.h: In static member function 'static void bpp::SymbolListTools::getCounts(const bpp::SymbolList&, std::map<int, double>&, 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,
^~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:50:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:136:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const OrderedSequenceContainer& sequences, const SequenceSelection& selection, SequenceContainer& outputCont) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:155:168: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const SequenceContainer& sequences, const std::vector<std::string>& selection, SequenceContainer& outputCont, bool strict = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:217:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:231:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:252:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:275:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:294:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/usr/include/c++/7/bits/stl_map.h: In static member function 'static void bpp::SymbolListTools::getFrequencies(const bpp::SymbolList&, std::map<int, double>&, 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,
^~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/usr/include/c++/7/bits/stl_map.h: In static member function 'static void bpp::SymbolListTools::getCounts(const bpp::SymbolList&, const bpp::SymbolList&, std::map<int, std::map<int, double> >&, 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,
^~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/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,
^~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:71:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceContainer& outputCont) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:97:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceContainer& outputCont, bool strict) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:204:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceContainer* SequenceContainerTools::getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException)
^~~~~
[ 62%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp
/usr/include/c++/7/bits/stl_map.h: In static member function 'static void bpp::SymbolListTools::getFrequencies(const bpp::SymbolList&, const bpp::SymbolList&, std::map<int, std::map<int, double> >&, 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,
^~~
[ 63%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp
[ 64%] Linking CXX static library libbpp-seq.a
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -P CMakeFiles/bpp-seq-static.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-seq-static.dir/link.txt --verbose=1
/usr/bin/ar qc libbpp-seq.a CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o
/usr/bin/ranlib libbpp-seq.a
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 64%] Built target bpp-seq-static
[ 65%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerIterator.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:158:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:166:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:265:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:321:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:350:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:367:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:418:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:469:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:136:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const OrderedSequenceContainer& sequences, const SequenceSelection& selection, SequenceContainer& outputCont) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:155:168: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const SequenceContainer& sequences, const std::vector<std::string>& selection, SequenceContainer& outputCont, bool strict = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:217:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:231:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:252:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:275:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:294:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:52:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:158:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& VectorSequenceContainer::getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:181:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& VectorSequenceContainer::getSequence(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:194:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& VectorSequenceContainer::getSequence_(size_t sequenceIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:204:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& VectorSequenceContainer::getSequence_(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:217:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t VectorSequenceContainer::getSequencePosition(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:230:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSequenceContainer::setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:258:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* VectorSequenceContainer::removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:272:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSequenceContainer::deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:284:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSequenceContainer::addSequence(const Sequence& sequence, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:307:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSequenceContainer::addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:347:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:384:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSequenceContainer::setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:341:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SiteContainer* SiteContainerTools::removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:360:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SiteContainerTools::removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:377:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:480:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:579:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:680:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:841:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double SiteContainerTools::computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist, const std::string& gapOption, bool unresolvedAsGap) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:940:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception)
^~~~~
In file included from /usr/include/c++/7/map:60:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.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 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 /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40:
/usr/include/c++/7/bits/stl_map.h: In static member function 'static void bpp::SequenceContainerTools::getFrequencies(const bpp::SequenceContainer&, std::map<int, double>&, 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,
^~~
[ 65%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp
[ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:56:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:290:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& VectorSiteContainer::getSite(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:299:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::setSite(size_t pos, const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:329:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* VectorSiteContainer::removeSite(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:340:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::deleteSite(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:350:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:363:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::addSite(const Site& site, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:392:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::addSite(const Site& site, int position, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:421:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::addSite(const Site& site, size_t siteIndex, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:454:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::addSite(const Site& site, size_t siteIndex, int position, bool checkPositions) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:529:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& VectorSiteContainer::getSequence(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:549:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& VectorSiteContainer::getSequence(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:571:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t VectorSiteContainer::getSequencePosition(const string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:584:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::setSequence(const string& name, const Sequence& sequence, bool checkNames) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:594:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:82:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:83:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:84:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:88:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:89:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.h:90:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:637:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* VectorSiteContainer::removeSequence(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:47:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int DNAToRNA::translate(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:55:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string DNAToRNA::translate(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:63:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int DNAToRNA::reverse(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DNAToRNA.cpp:71:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string DNAToRNA::reverse(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:663:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* VectorSiteContainer::removeSequence(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:672:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::deleteSequence(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:693:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::deleteSequence(const string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:702:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::addSequence(const Sequence& sequence, bool checkNames) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:746:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:835:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.cpp:859:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void VectorSiteContainer::setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException)
^~~~~
[ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.cpp
[ 67%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:86:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:92:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:97:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h:103:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/DistanceMatrix.cpp:45:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t DistanceMatrix::getNameIndex(const std::string& name) const throw (Exception)
^~~~~
[ 67%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:89:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:94:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:100:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
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/VectorTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.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<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/VectorTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.cpp:41:
/usr/include/c++/7/bits/stl_map.h: In static member function 'static bpp::SiteContainer* bpp::SiteContainerTools::removeGapSites(const bpp::SiteContainer&, double)':
/usr/include/c++/7/bits/stl_map.h:512:4: 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: In static member function 'static void bpp::SiteContainerTools::removeGapSites(bpp::SiteContainer&, double)':
/usr/include/c++/7/bits/stl_map.h:512:4: 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,
^~~
[ 68%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
[ 68%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
[ 69%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
[ 69%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp
[ 70%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:86:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:92:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:97:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h:103:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
[ 71%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
[ 71%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:84:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isStop(const std::string& state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:95:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(int state) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:101:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isAltStart(const std::string& state) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:82:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IAlignment* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:111:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:122:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:125:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:136:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:143:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:144:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:184:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:185:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:186:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:75:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:89:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:103:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:113:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:114:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:76:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:87:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:101:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:112:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:115:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:144:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence_(const std::string & s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:56:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IAlignment* BppOAlignmentReaderFormat::read(const std::string& description) throw (Exception)
^~~~~
[ 72%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp
[ 72%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AlphabetIndex1.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h:107:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex1* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:84:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OAlignment* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:75:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:89:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:103:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:113:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:114:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:111:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:122:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:125:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:136:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:143:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:144:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:184:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:185:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:186:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:83:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:84:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:55:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OAlignment* BppOAlignmentWriterFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAPolarityIndex.h:106:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAPolarityIndex.h:112:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAVolumeIndex.h:109:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAVolumeIndex.h:115:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/KleinAANetChargeIndex.h:106:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/KleinAANetChargeIndex.h:112:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanAHelixIndex.h:92:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanAHelixIndex.h:98:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanBSheetIndex.h:92:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanBSheetIndex.h:98:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanTurnIndex.h:92:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChouFasmanTurnIndex.h:98:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h:104:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h:110:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:49:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASurfaceIndex.h:90:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:49:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASurfaceIndex.h:96:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAMassIndex.h:90:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAMassIndex.h:96:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:51:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAVolumeIndex.h:92:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:51:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAVolumeIndex.h:98:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:52:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChargeIndex.h:133:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:52:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAChargeIndex.h:139:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:53:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEAInf10Index.h:90:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEAInf10Index.h:96:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:54:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEA1030Index.h:90:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEA1030Index.h:96:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:55:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEASup30Index.h:90:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AASEASup30Index.h:96:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:56:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex1Entry.h:65:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex1Entry(std::istream& input) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex1Entry.h:84:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex1Entry.h:90:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp:67:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex1* BppOAlphabetIndex1Format::read(const std::string& description) throw (Exception)
^~~~~
[ 73%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AlphabetIndex2.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.h:107:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex2* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h:107:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex1* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
[ 73%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/BLOSUM50.h:94:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/BLOSUM50.h:95:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAChemicalDistance.h:132:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/GranthamAAChemicalDistance.h:133:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/MiyataAAChemicalDistance.h:103:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/MiyataAAChemicalDistance.h:104:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/SimpleIndexDistance.h:89:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/SimpleIndexDistance.h:95:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex2Entry.h:72:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AAIndex2Entry(std::istream& input, bool sym = true) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex2Entry.h:95:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(int state1, int state2) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../AlphabetIndex/AAIndex2Entry.h:102:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp:59:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetIndex2* BppOAlphabetIndex2Format::read(const std::string& description) throw (Exception)
^~~~~
[ 74%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:83:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequence* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:111:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:122:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:125:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:136:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:143:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:144:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:184:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:185:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:186:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:75:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:89:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:103:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:113:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:114:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:76:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:87:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:75:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:101:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:112:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:115:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:144:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence_(const std::string & s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:57:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequence* BppOSequenceReaderFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:81:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequenceStream* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:51:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequenceStream* BppOSequenceStreamReaderFormat::read(const std::string& description) throw (Exception)
^~~~~
[ 74%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp
[ 75%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
[ 75%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:82:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OSequence* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:52:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OSequence* BppOSequenceWriterFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:75:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:89:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:103:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:113:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:114:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:52:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Clustal::appendAlignmentFromStream(std::istream& input, SiteContainer & sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.cpp:114:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Clustal::writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
[ 76%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:76:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:87:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.cpp:52:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DCSE::appendAlignmentFromStream(istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:56:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool Fasta::nextSequence(istream& input, Sequence& seq) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:116:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::writeSequence(ostream& output, const Sequence& seq) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:147:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::appendSequencesFromStream(istream& input, SequenceContainer& vsc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:204:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::writeSequences(ostream& output, const SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:231:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::FileIndex::build(const std::string& path, const bool strictSequenceNames) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:255:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
streampos Fasta::FileIndex::getSequencePosition(const std::string& id) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:263:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::FileIndex::read(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.cpp:277:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Fasta::FileIndex::write(const std::string& path) throw (Exception) {
^~~~~
[ 76%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
[ 77%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:75:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
[ 78%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.cpp:50:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void GenBank::appendSequencesFromStream(std::istream& input, SequenceContainer& vsc) const throw (Exception)
^~~~~
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:90:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISequence* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:99:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:108:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSequence* createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.h:117:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:75:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:89:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:103:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:113:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:114:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:76:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:87:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Dcse.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:111:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:122:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:125:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:136:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:143:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:144:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:184:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:185:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:186:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/GenBank.h:75:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:101:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:112:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:115:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:144:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence_(const std::string & s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:63:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISequence* IoSequenceFactory::createReader(const string& format) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:78:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IAlignment* IoSequenceFactory::createAlignmentReader(const string& format) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:92:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OSequence* IoSequenceFactory::createWriter(const string& format) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/IoSequenceFactory.cpp:99:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OAlignment* IoSequenceFactory::createAlignmentWriter(const string& format) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:49:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Mase::appendSequencesFromStream(std::istream& input, SequenceContainer& vsc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:119:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Mase::writeSequences(ostream& output, const SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.cpp:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Mase::readHeader_(std::istream& input, MaseHeader& header) const throw (Exception)
^~~~~
[ 78%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
[ 79%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:136:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const OrderedSequenceContainer& sequences, const SequenceSelection& selection, SequenceContainer& outputCont) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:155:168: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const SequenceContainer& sequences, const std::vector<std::string>& selection, SequenceContainer& outputCont, bool strict = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:217:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:231:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:252:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:275:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:294:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:158:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:166:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:265:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:321:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:350:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:367:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:418:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:469:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:74:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteSelection getSiteSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:83:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceSelection getSequenceSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:97:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSelectedSites(const SiteContainer& sequences, const std::string& setName) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:111:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getSelectedSequences(const OrderedSequenceContainer& sequences, const std::string & setName) throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.h:139:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getPhase(const Comments & maseFileHeader, const std::string &setName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:52:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SiteSelection MaseTools::getSiteSet(const Comments& maseFileHeader, const string& setName) throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:104:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceSelection MaseTools::getSequenceSet(const Comments& maseFileHeader, const string& setName) throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:153:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const string& setName) throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:163:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& setName) throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/MaseTools.cpp:246:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t MaseTools::getPhase(const Comments& maseFileHeader, const string& setName) throw (Exception)
^~~~~
[ 79%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusTools.h:77:117: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool getNextCommand(std::istream& input, std::string& name, std::string& arguments, bool lineBrk = true) throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:101:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:112:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:115:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.h:144:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence_(const std::string & s) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusTools.h:77:117: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool getNextCommand(std::istream& input, std::string& name, std::string& arguments, bool lineBrk = true) throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusTools.cpp:73:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:158:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:166:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:265:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:321:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:350:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:367:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:418:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainerTools.h:469:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:57:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> NexusIOSequence::splitNameAndSequence_(const std::string& s) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/NexusIoSequence.cpp:70:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOSequence::appendAlignmentFromStream(std::istream& input, SiteContainer& vsc) const throw (Exception)
^~~~~
[ 80%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:194:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:258:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:285:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:312:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:343:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:366:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:393:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:420:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:451:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:487:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:537:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:554:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:568:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQualities(const std::vector<int>& quality) throw (DimensionException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:599:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:623:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:647:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:660:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:676:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:683:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:702:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:709:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:723:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:730:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:747:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:97:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.h:116:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:52:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool PhredPhd::nextSequence(std::istream& input, Sequence& seq) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPhd.cpp:59:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool PhredPhd::nextSequence(std::istream& input, Sequence& seq, std::vector<int>& pos) const throw (Exception) {
^~~~~
[ 80%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp
[ 81%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp
[ 81%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.h:74:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
[ 82%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/PhredPoly.cpp:54:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool PhredPoly::nextSequence(istream& input, Sequence& seq) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:111:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:122:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:125:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:136:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:143:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:144:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:184:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:185:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:186:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:136:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const OrderedSequenceContainer& sequences, const SequenceSelection& selection, SequenceContainer& outputCont) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:155:168: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getSelectedSequences(const SequenceContainer& sequences, const std::vector<std::string>& selection, SequenceContainer& outputCont, bool strict = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:217:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:231:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:252:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:275:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainerTools.h:294:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceContainer* getCodonPosition(const SequenceContainer& sequences, size_t pos) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:55:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> Phylip::splitNameAndSequence(const std::string& s) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Phylip::readSequential(std::istream& in, SiteContainer& asc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:132:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Phylip::readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:174:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Phylip::appendAlignmentFromStream(std::istream& input, SiteContainer& vsc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:185:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int Phylip::getNumberOfSequences(const std::string& path) const throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.cpp:279:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Phylip::writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:83:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.h:84:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Stockholm.cpp:54:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Stockholm::writeAlignment(ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceIterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:194:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:258:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:285:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:312:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:343:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:366:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:393:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:420:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:451:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:487:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:537:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:554:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:568:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQualities(const std::vector<int>& quality) throw (DimensionException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:599:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:623:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:647:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:660:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:676:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:683:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:702:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:709:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:723:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:730:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SequenceWithQuality.h:747:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/StreamSequenceIterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
[ 82%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp
[ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Sequence.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:70:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int NucleicAcidsReplication::translate(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:76:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string NucleicAcidsReplication::translate(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:82:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* NucleicAcidsReplication::translate(const Sequence& sequence) const throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:96:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int NucleicAcidsReplication::reverse(int state) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:102:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string NucleicAcidsReplication::reverse(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.cpp:108:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* NucleicAcidsReplication::reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:65:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:78:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:90:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:100:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:109:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:119:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:156:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSequence::setContent(const std::string& sequence) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:205:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSequence::append(const Sequence& seq) throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:214:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSequence::append(const std::vector<int>& content) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:225:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSequence::append(const std::vector<std::string>& content) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.cpp:237:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSequence::append(const std::string& content) throw (BadCharException)
^~~~~
[ 84%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.cpp
[ 84%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceExceptions.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
[ 85%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
[ 85%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequencePositionIterators.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
[ 86%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
[ 86%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:81:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getAlignmentPosition(size_t seqPos) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:82:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(size_t alnPos) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:49:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t SequenceWalker::getAlignmentPosition(size_t seqPos) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.cpp:81:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t SequenceWalker::getSequencePosition(size_t alnPos) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:88:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::concatenate(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:108:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& SequenceTools::complement(Sequence& seq) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:133:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::getComplement(const Sequence& sequence) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:155:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::transcript(const Sequence& sequence) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:168:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::reverseTranscript(const Sequence& sequence) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:245:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double SequenceTools::getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps) throw (AlphabetMismatchException, SequenceNotAlignedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:365:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:383:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceTools::removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:397:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceTools::replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:413:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (SequenceNotAlignedException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:518:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:543:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::subtractHaplotype(const Sequence& s, const Sequence& h, string name, unsigned int level) throw (SequenceNotAlignedException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:577:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::RNYslice(const Sequence& seq, int ph) throw (AlphabetException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.cpp:619:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* SequenceTools::RNYslice(const Sequence& seq) throw (AlphabetException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
[ 87%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:62:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:72:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:82:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:89:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:96:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:103:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:143:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceWithAnnotation::setContent(const std::string& sequence) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:206:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceWithAnnotation::append(const Sequence& seq) throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:218:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceWithAnnotation::append(const std::vector<int>& content) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:233:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceWithAnnotation::append(const std::vector<std::string>& content) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:249:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SequenceWithAnnotation::append(const std::string& content) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.cpp:270:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:174:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation* createMaskAnnotation(const Sequence& seq) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:108:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getMaskedEquivalentState(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h:117:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string getMaskedEquivalentState(const std::string& state) const throw (BadCharException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotationTools.cpp:74:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation* SequenceWithAnnotationTools::createMaskAnnotation(const Sequence& seq) throw (AlphabetException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:194:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:258:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:285:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:312:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:343:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:366:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:393:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:420:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:451:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:487:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:537:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:554:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:568:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQualities(const std::vector<int>& quality) throw (DimensionException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:599:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:623:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:647:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:660:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:676:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:683:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:702:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:709:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:723:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:730:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:747:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
[ 87%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp
[ 88%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Site.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:58:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site::Site(const vector<string>& site, const Alphabet* alpha) throw (BadCharException) : AbstractCoreSite(), BasicSymbolList(site, alpha) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:60:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site::Site(const vector<string>& site, const Alphabet* alpha, int position) throw (BadCharException) : AbstractCoreSite(position), BasicSymbolList(site, alpha) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:62:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site::Site(const vector<int>& site, const Alphabet* alpha) throw (BadIntException) : AbstractCoreSite(), BasicSymbolList(site, alpha) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.cpp:64:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site::Site(const vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException) : AbstractCoreSite(position), BasicSymbolList(site, alpha) {}
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:98:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:158:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:174:131: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:186:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:199:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:208:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:218:136: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:314:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:315:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:319:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:335:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:337:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:339:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:341:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:354:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithAnnotation.h:409:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:194:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:258:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:285:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (BadCharException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:312:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:343:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:366:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:393:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:420:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:451:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:487:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (DimensionException):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:537:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:554:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:568:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setQualities(const std::vector<int>& quality) throw (DimensionException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:599:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:623:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:647:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:660:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:676:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:683:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:702:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:709:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:723:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:730:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQuality.h:747:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:77:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const SequenceWithQuality& sequence, size_t begin, size_t end, SequenceWithQuality& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:97:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SequenceWithQuality* subseq(const SequenceWithQuality& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:122:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetMismatchException, Exception) ;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:135:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:148:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.h:162:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:54:130: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithQuality* SequenceWithQualityTools::concatenate(const SequenceWithQuality& seqwq1, const SequenceWithQuality& seqwq2) throw (AlphabetMismatchException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:77:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithQuality* SequenceWithQualityTools::complement(const SequenceWithQuality& sequence) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:101:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithQuality* SequenceWithQualityTools::transcript(const SequenceWithQuality& sequence) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWithQualityTools.cpp:116:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SequenceWithQuality* SequenceWithQualityTools::reverseTranscript(const SequenceWithQuality& sequence) throw (AlphabetException)
^~~~~
[ 88%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteExceptions.cpp
[ 89%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp
[ 90%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteExceptions.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteExceptions.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteExceptions.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
[ 90%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:83:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string subseq(const std::string& sequence, size_t begin, size_t end) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:160:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCcontent(const std::string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:176:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> codeSequence(const std::string& sequence, const Alphabet* alphabet) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:186:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string decodeSequence(const std::vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.h:197:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Alphabet* getAlphabetFromSequence(const std::string& sequence) throw (EmptySequenceException, SequenceException, AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:49:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList::BasicSymbolList(const std::vector<string>& list, const Alphabet* alpha) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:61:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string StringSequenceTools::subseq(const string& sequence, size_t begin, size_t end) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:55:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList::BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:194:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double StringSequenceTools::getGCcontent(const string& sequence, size_t pos, size_t window) throw (BadIntegerException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:91:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::setContent(const vector<string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:107:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::setContent(const vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:127:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::addElement(const string& c) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:134:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::addElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:142:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::setElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string BasicSymbolList::getChar(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:169:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::deleteElement(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:178:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:187:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::addElement(int v) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:196:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:207:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BasicSymbolList::setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:218:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int BasicSymbolList::getValue(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:230:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList::EdSymbolList(const std::vector<string>& list, const Alphabet* alpha) throw (BadCharException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:236:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList::EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:273:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:290:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string StringSequenceTools::decodeSequence(const vector<int>& sequence, const Alphabet* alphabet) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:291:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::setContent(const vector<string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/StringSequenceTools.cpp:303:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (EmptySequenceException, SequenceException, AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:311:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::setContent(const vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:335:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::addElement(const string& c) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:345:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::addElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:356:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::setElement(size_t pos, const string& c) throw (BadCharException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:368:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string EdSymbolList::getChar(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:383:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::deleteElement(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:395:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:408:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::addElement(int v) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:420:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:434:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void EdSymbolList::setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.cpp:448:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int EdSymbolList::getValue(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
[ 91%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.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 /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.cpp:41:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static double bpp::SiteTools::heterozygosity(const bpp::Site&)':
/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);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 91%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_seq_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-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Transliterator.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:69:144: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SymbolListTools::getCounts(const SymbolList& list1, const SymbolList& list2, map< int, map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:103:152: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SymbolListTools::getFrequencies(const SymbolList& list1, const SymbolList& list2, map<int, map<int, double> >& frequencies, bool resolveUnknowns) throw (DimensionException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:115:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double SymbolListTools::getGCContent(const SymbolList& list, bool ignoreUnresolved, bool ignoreGap) throw (AlphabetException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:154:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t SymbolListTools::getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:165:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t SymbolListTools::getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException)
^~~~~
In file included from /usr/include/c++/7/map:60:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.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 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 /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.cpp:40:
/usr/include/c++/7/bits/stl_map.h: In static member function 'static void bpp::SymbolListTools::getCounts(const bpp::SymbolList&, std::map<int, double>&, 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,
^~~
/usr/include/c++/7/bits/stl_map.h: In static member function 'static void bpp::SymbolListTools::getFrequencies(const bpp::SymbolList&, std::map<int, double>&, 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: In static member function 'static void bpp::SymbolListTools::getCounts(const bpp::SymbolList&, const bpp::SymbolList&, std::map<int, std::map<int, double> >&, 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,
^~~
/usr/include/c++/7/bits/stl_map.h: In static member function 'static void bpp::SymbolListTools::getFrequencies(const bpp::SymbolList&, const bpp::SymbolList&, std::map<int, std::map<int, double> >&, 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,
^~~
[ 92%] Linking CXX shared library libbpp-seq.so
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-seq-shared.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -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 -shared -Wl,-soname,libbpp-seq.so.11 -o libbpp-seq.so.11.0.0 CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o /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-seq.so.11.0.0 libbpp-seq.so.11 libbpp-seq.so
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[ 92%] Built target bpp-seq-shared
make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.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_alphabets.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_alignment_scores.dir/DependInfo.cmake --color=
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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_bowker.dir/DependInfo.cmake --color=
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[ 93%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.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_alphabets.dir/test_alphabets.cpp.o -c /<<PKGBUILDDIR>>/test/test_alphabets.cpp
[ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o
[ 94%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.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
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_alignment_scores.dir/test_alignment_scores.cpp.o -c /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp
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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_io.dir/test_io.cpp.o -c /<<PKGBUILDDIR>>/test/test_io.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/test/test_io.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_bowker.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:43:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:46,
from /<<PKGBUILDDIR>>/test/test_io.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alphabets.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43:0,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:46:0,
from /<<PKGBUILDDIR>>/test/test_io.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_io.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:43,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_bowker.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:81:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:90:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:116:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequence.h:125:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(std::istream& input, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:94:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readSequences(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:106:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readSequences(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:123:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:132:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendSequencesFromFile(const std::string& path, SequenceContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:147:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:45:0,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractISequence.h:161:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual VectorSequenceContainer* readSequencesFromFile(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:81:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(std::istream& input, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:93:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void readAlignment(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:99:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(const std::string& path , const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:105:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:124:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:133:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void appendAlignmentFromFile(const std::string& path, SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:148:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromStream(std::istream& input, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:46:0,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractIAlignment.h:163:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlignedSequenceContainer* readAlignmentFromFile(const std::string& path, const Alphabet* alpha) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:74:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:85:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:111:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequence.h:122:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:47:0,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:73:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:74:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:92:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOSequence.h:96:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:51:0,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/ISequenceStream.h:75:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:52:0,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/OSequenceStream.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:53:0,
from /<<PKGBUILDDIR>>/test/test_io.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:61:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void build(const std::string& path) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:66:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::streampos getSequencePosition(const std::string& id) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/SequenceFileIndex.h:71:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNumberOfSequences() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_io.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:110:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:120:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:122:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite=true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:145:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:153:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:188:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:197:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void build(const std::string& path, const bool strictSequenceNames) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:198:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::streampos getSequencePosition(const std::string& id) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:199:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfSequences() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:205:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Fasta.h:209:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::string& path) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_io.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:81:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getTree(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:88:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const MultiRange<size_t>& getSiteSelection(const std::string& name) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:95:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<size_t>& getSequenceSelection(const std::string& name) const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_io.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:158:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::istream& input, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:163:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSequenceContainer* readMeta(std::string& path, const Alphabet* alpha, MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:177:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendSequencesFromStream(std::istream& input, SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:185:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:196:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:197:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeSequences(const std::string& path, const SequenceContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:208:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(std::ostream& output, const SequenceContainer& sc, const MaseHeader& header) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:213:129: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeMeta(const std::string& path, const SequenceContainer& sc, const MaseHeader& header, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Mase.h:249:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readHeader_(std::istream& input, MaseHeader& header) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:44:0,
from /<<PKGBUILDDIR>>/test/test_io.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:72:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/AbstractOAlignment.h:73:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_io.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:75:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:89:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:100:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:103:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:113:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Clustal.h:114:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_io.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:111:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:122:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:125:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:136:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:143:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:144:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:184:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:185:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Io/Phylip.h:186:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:158:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:166:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:265:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:321:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:350:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:367:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:418:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:469:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SiteTools.h:44:0,
from /<<PKGBUILDDIR>>/test/test_alignment_scores.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
[ 95%] Linking CXX executable test_alphabets
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alphabets.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_alphabets.dir/test_alphabets.cpp.o -o test_alphabets -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/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_alphabets
make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.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_containers.dir/DependInfo.cmake --color=
Scanning dependencies of target test_containers
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 96%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.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_containers.dir/test_containers.cpp.o -c /<<PKGBUILDDIR>>/test/test_containers.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43:0,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_containers.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:43,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:43:0,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:92:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:103:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<std::string>& site, const Alphabet* alpha, int position) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:113:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Site.h:124:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site(const std::vector<int>& site, const Alphabet* alpha, int position) throw (BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:102:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:111:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:130:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:144:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:153:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:162:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:188:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string>& names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:198:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:208:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:264:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SequenceContainer.h:276:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:72:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:82:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:94:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:103:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:112:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:122:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:132:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:142:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:151:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:163:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:165:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:176:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:187:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:221:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:222:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:223:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:224:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:225:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:228:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:229:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/OrderedSequenceContainer.h:230:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
^~~~~
[ 96%] 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-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:44:0,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:80:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:90:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:109:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:119:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:130:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:141:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainer.h:158:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:45:0,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:125:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string toString(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:130:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:158:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:163:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:168:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AbstractSequenceContainer.h:173:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:87:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:170:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:180:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:188:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:192:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:197:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:212:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:217:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:238:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:243:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:244:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:245:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:246:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:247:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:248:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:271:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:289:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:298:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSequenceContainer.h:299:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:46:0,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:140:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlignedSequenceContainer& operator=(const OrderedSequenceContainer& osc) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:159:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:160:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:161:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site * removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:162:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:163:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:164:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:165:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:166:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:167:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:180:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:181:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:183:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/AlignedSequenceContainer.h:184:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:89:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
VectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha, bool checkPositions = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_containers.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:138:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:139:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSite(size_t siteIndex, const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:140:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:141:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:142:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:143:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:144:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:145:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:146:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:160:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:163:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:164:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:169:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:171:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:172:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:174:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:175:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:181:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:192:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:206:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:212:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:228:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:229:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:231:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/VectorSiteContainer.h:232:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:147:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:160:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:172:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNames(const std::vector<std::string>& names) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:185:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNameIndex(const std::string& name) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:209:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../DistanceMatrix.h:225:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/GeneticCode.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:48,
from /<<PKGBUILDDIR>>/test/test_containers.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/../GeneticCode/../Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
[ 96%] Built target test_bowker
make -f test/CMakeFiles/test_walker.dir/build.make test/CMakeFiles/test_walker.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_walker.dir/DependInfo.cmake --color=
In file included from /<<PKGBUILDDIR>>/test/test_containers.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:158:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_containers.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:166:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStopCodonSites(SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:265:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:321:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:350:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:367:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:418:184: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_containers.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Container/SiteContainerTools.h:469:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);
^~~~~
Scanning dependencies of target test_walker
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_walker.dir/build.make test/CMakeFiles/test_walker.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 97%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.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_walker.dir/test_walker.cpp.o -c /<<PKGBUILDDIR>>/test/test_walker.cpp
[ 98%] Linking CXX executable test_alignment_scores
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alignment_scores.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_alignment_scores.dir/test_alignment_scores.cpp.o -o test_alignment_scores -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/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_alignment_scores
make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.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_sequences.dir/DependInfo.cmake --color=
Scanning dependencies of target test_sequences
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 99%] Building CXX object test/CMakeFiles/test_sequences.dir/test_sequences.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_sequences.dir/test_sequences.cpp.o -c /<<PKGBUILDDIR>>/test/test_sequences.cpp
[ 99%] Linking CXX executable test_io
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_io.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_io.dir/test_io.cpp.o -o test_io -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/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_io
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:44:0,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_sequences.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:86:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:88:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DNA.h:89:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:44:0,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:45:0,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:68:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:76:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:86:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:126:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:127:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:128:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:129:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:147:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(const std::string & aa) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/ProteicAlphabet.h:154:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getAbbr(int aa) const throw (AlphabetException);
^~~~~
[ 99%] Linking CXX executable test_containers
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:46:0,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/DefaultAlphabet.h:58:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_containers.dir/link.txt --verbose=1
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_walker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:157:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:169:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:175:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:181:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:186:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:191:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:231:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:242:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:251:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:268:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:277:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:335:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:346:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:358:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/Alphabet.h:371:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
^~~~~
/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_containers.dir/test_containers.cpp.o -o test_containers -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_walker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:146:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:147:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:148:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:151:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:152:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:153:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:154:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:176:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:187:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:198:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:200:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(const std::string& letter) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:211:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const AlphabetState& getState(int num) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:213:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
AlphabetState& getState(int num) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:215:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:219:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:223:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:225:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getStateIndex(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:235:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void registerState(AlphabetState* st) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AbstractAlphabet.h:245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43,
from /<<PKGBUILDDIR>>/test/test_walker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:91:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string &state) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:98:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/LetterAlphabet.h:108:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:43:0,
from /<<PKGBUILDDIR>>/test/test_walker.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:92:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerState(AlphabetState* st) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:100:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:116:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:122:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IndexOutOfBoundsException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:128:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:134:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:155:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:183:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int subtract(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:207:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:232:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getOverlap(int s1, int s2) const throw (BadIntException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/NucleicAlphabet.h:256:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/../Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_walker.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:84:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:85:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string & state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:86:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int> & states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNA.h:87:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string> & states) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:125:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getName(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:127:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:181:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:182:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:183:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:184:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:192:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsUnresolved(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:227:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:239:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:251:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:260:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNPosition(int word, size_t n) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:276:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getPositions(int word) const throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:294:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:312:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:333:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/WordAlphabet.h:343:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:126:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:134:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFirstPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getSecondPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:150:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getThirdPosition(int codon) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:158:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:166:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/CodonAlphabet.h:174:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:48:0,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:90:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int charToInt(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:91:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string intToChar(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:93:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsGap(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:99:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int > getAlias( int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:100:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:119:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getRNY(const std::string&, const std::string&, const std::string&) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/RNY.h:121:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getRNY(int, int, int, const Alphabet&) const throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:49:0,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:83:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAlias(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/BinaryAlphabet.h:84:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
^~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:44:0,
from /<<PKGBUILDDIR>>/test/test_walker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:105:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:113:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:137:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:145:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:153:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:160:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:168:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:176:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:183:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:191:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:199:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:206:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:289:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:299:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:338:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:344:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:346:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:348:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:350:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:352:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
[ 99%] Built target test_containers
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:354:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:356:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:358:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:360:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:362:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:524:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<std::string>& list, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:534:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
EdSymbolList(const std::vector<int>& list, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:582:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:584:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:588:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(const std::string& c) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:590:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:592:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, const std::string& c) throw (BadCharException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:594:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElement(size_t pos) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:596:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteElements(size_t pos, size_t len) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:598:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getChar(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:600:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(int v) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:602:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:604:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setElement(size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolList.h:606:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getValue(size_t pos) const throw (IndexOutOfBoundsException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_walker.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:93:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:94:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:122:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const Sequence& seq) throw (AlphabetMismatchException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:130:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:138:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:146:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void append(const std::string& content) throw (BadCharException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:196:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:212:122: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_walker.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:224:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:237:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:246:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:256:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:300:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::string& sequence) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:302:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<int>& list) throw (BadIntException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:307:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setContent(const std::vector<std::string>& list) throw (BadCharException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:316:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const Sequence& seq) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:318:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<int>& content) throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:320:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::vector<std::string>& content) throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Sequence.h:322:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void append(const std::string& content) throw (BadCharException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_walker.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:81:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getAlignmentPosition(size_t seqPos) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceWalker.h:82:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSequencePosition(size_t alnPos) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_sequences.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:103:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:114:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:123:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Alphabet/AlphabetTools.h:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:88:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:51:0,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:126:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:149:164: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:160:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:172:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SymbolListTools.h:184:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:52:0,
from /<<PKGBUILDDIR>>/test/test_sequences.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:93:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int translate(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:94:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string translate(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:95:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* translate(const Sequence& sequence) const throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:96:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int reverse(int state) const throw (BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:97:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string reverse(const std::string& state) const throw (BadCharException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/NucleicAcidsReplication.h:98:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_sequences.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:128:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void subseq(const Sequence& sequence, size_t begin, size_t end, Sequence& output) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_sequences.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:146:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:169:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (AlphabetMismatchException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:179:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence& complement(Sequence& seq) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:189:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:201:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:213:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:260:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:323:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void removeStops(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:336:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* getSequenceWithoutStops(const Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:346:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void replaceStopsWithGaps(Sequence& seq, const GeneticCode& gCode) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:363:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:385:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:412:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:428:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/SequenceTools.h:429:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);
^~~~~
[100%] Linking CXX executable test_walker
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_walker.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_walker.dir/test_walker.cpp.o -o test_walker -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/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_walker
[100%] Linking CXX executable test_sequences
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sequences.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_sequences.dir/test_sequences.cpp.o -o test_sequences -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/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_sequences
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_alignment_scores
Start 2: test_alphabets
Start 3: test_bowker
Start 4: test_containers
1/7 Test #1: test_alignment_scores ............ Passed 0.02 sec
2/7 Test #2: test_alphabets ................... Passed 0.12 sec
3/7 Test #4: test_containers .................. Passed 0.11 sec
Start 5: test_io
Start 6: test_sequences
Start 7: test_walker
4/7 Test #6: test_sequences ................... Passed 0.10 sec
5/7 Test #7: test_walker ...................... Passed 0.10 sec
6/7 Test #5: test_io .......................... Passed 0.16 sec
7/7 Test #3: test_bowker ...................... Passed 45.51 sec
100% tests passed, 0 tests failed out of 7
Total Test time (real) = 45.52 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-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/depend
make -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-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-seq-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-seq-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-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/build
make -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-static.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/CMakeFiles/bpp-seq-shared.dir/build'.
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/CMakeFiles/bpp-seq-static.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 92%] Built target bpp-seq-static
[ 92%] Built target bpp-seq-shared
make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/depend
make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.dir/depend
make -f test/CMakeFiles/test_io.dir/build.make test/CMakeFiles/test_io.dir/depend
make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.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_alphabets.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 93%] Built target test_alphabets
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make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/depend
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 98%] Built target test_walker
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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-seq/bpp-seq-config.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-seq/bpp-seq-config-version.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-seq.a
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-seq.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/CodonSiteTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SymbolListTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SiteTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SequenceWithAnnotationTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/CoreSequence.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SequenceWalker.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/IntegerAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/RNY.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/DNA.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/WordAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/ProteicAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/CodonAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/NucleicAlphabetState.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/RNA.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetState.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetNumericState.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/NumericAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/LexicalAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/ProteicAlphabetState.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetExceptions.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/BinaryAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/DefaultAlphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Alphabet/Alphabet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SequenceExceptions.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SymbolList.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SequenceIterator.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Sequence.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/CoreSite.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/NucleicAcidsReplication.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/NexusIoSequence.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/SequenceFileIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/OSequence.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/OSequenceStream.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlignmentReaderFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/IoSequenceStream.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/Mase.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/ISequenceStream.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/PhredPhd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/IoSequence.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/PhredPoly.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/Clustal.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/AbstractISequence.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/Phylip.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/ISequence.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/Dcse.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/AbstractIAlignment.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceWriterFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/Stockholm.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlphabetIndex1Format.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/NexusTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlignmentWriterFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/StreamSequenceIterator.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/AbstractOAlignment.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/IoSequenceFactory.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/MaseTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceReaderFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/AbstractOSequence.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlphabetIndex2Format.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/GenBank.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Io/Fasta.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/GeneticCode
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/GeneticCode/GeneticCode.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/GeneticCode/StandardGeneticCode.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SequencePositionIterators.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SequenceTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASEASup30Index.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/BLOSUM50.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAMassIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/SimpleScore.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/UserAlphabetIndex1.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChargeIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASEA1030Index.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/DistanceMatrix.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SequenceWithQuality.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SequenceWithAnnotation.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SiteExceptions.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SiteIterator.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/SequenceWithQualityTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/App
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/App/SequenceApplicationTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/DNAToRNA.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Site.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Transliterator.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/StringSequenceTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/AlignedSequenceContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/SequenceContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerIterator.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/AbstractSequenceContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/SequenceContainerIterator.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/VectorSequenceContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerExceptions.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/SequenceContainerExceptions.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/MapSequenceContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/SequenceContainerTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/VectorSiteContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/CompressedVectorSiteContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Seq/Container/OrderedSequenceContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-seq/bpp-seq-targets.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-seq/bpp-seq-targets-none.cmake
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# Broken header, don't install (if we do, the postinst will pull it
# into generic include files)
rm -f debian/tmp/usr/include/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h
dh_install
d-shlibmove --commit \
--multiarch \
--devunversioned \
--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.
set -e
install -d -m 755 debian/libbpp-seq-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libbpp-seq11/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-seq.a debian/libbpp-seq-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-seq.so debian/libbpp-seq-dev/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11 debian/libbpp-seq11/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 debian/libbpp-seq11/usr/lib/arm-linux-gnueabihf
PKGDEV=libbpp-seq-dev
PKGSHL=libbpp-seq11
install -d -m 755 debian/libbpp-seq-dev/usr/include
mv debian/tmp/usr/include/Bpp debian/libbpp-seq-dev/usr/include
install -d -m 755 debian/libbpp-seq-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/cmake debian/libbpp-seq-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-seq11/usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 found in none of the libraries
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package libbpp-seq-dev: unused substitution variable ${devlibs:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libbpp-seq-dev' in '../libbpp-seq-dev_2.3.1-8_armhf.deb'.
dpkg-deb: building package 'libbpp-seq11' in '../libbpp-seq11_2.3.1-8_armhf.deb'.
dpkg-deb: building package 'libbpp-seq11-dbgsym' in '../libbpp-seq11-dbgsym_2.3.1-8_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../libbpp-seq_2.3.1-8_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build libbpp-seq-2.3.1
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-08-29T05:34:08Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
libbpp-seq_2.3.1-8_armhf.changes:
---------------------------------
Format: 1.8
Date: Wed, 23 Aug 2017 19:38:40 +0200
Source: libbpp-seq
Binary: libbpp-seq-dev libbpp-seq11
Architecture: armhf
Version: 2.3.1-8
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
libbpp-seq-dev - Bio++ Sequence library development files
libbpp-seq11 - Bio++ Sequence library
Changes:
libbpp-seq (2.3.1-8) unstable; urgency=medium
.
* Rebuild with gcc-7
* Standards-Version: 4.0.1
Checksums-Sha1:
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2802cc9fa543dba142caa1107e969e474c30f13e 7486194 libbpp-seq11-dbgsym_2.3.1-8_armhf.deb
0f43e9f4265890074c5596ec27d1954c331bfaeb 404716 libbpp-seq11_2.3.1-8_armhf.deb
1805fedc8203bdcda7aff7bfee4de9027cedaf45 6139 libbpp-seq_2.3.1-8_armhf.buildinfo
Checksums-Sha256:
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2891ed3c5ea34643fe4aa0e43d117d43f6dd184d6dcb19ca50cefe4a856f30f5 7486194 libbpp-seq11-dbgsym_2.3.1-8_armhf.deb
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7355c612698e4e027529898392739d852ab93d2704723a8a3c565a7b4932620e 6139 libbpp-seq_2.3.1-8_armhf.buildinfo
Files:
b59d948b9993bac1aeff00c49aea9808 704828 libdevel optional libbpp-seq-dev_2.3.1-8_armhf.deb
4bda86460ec580a38e55b9919756def3 7486194 debug extra libbpp-seq11-dbgsym_2.3.1-8_armhf.deb
c16801889b292f41b5dd3ad7e9462885 404716 libs optional libbpp-seq11_2.3.1-8_armhf.deb
25e968a4b53c0731e064febbae5d9579 6139 science optional libbpp-seq_2.3.1-8_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libbpp-seq-dev_2.3.1-8_armhf.deb
--------------------------------
new debian package, version 2.0.
size 704828 bytes: control archive=4679 bytes.
867 bytes, 19 lines control
10990 bytes, 135 lines md5sums
Package: libbpp-seq-dev
Source: libbpp-seq
Version: 2.3.1-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6338
Depends: libbpp-seq11 (= 2.3.1-8), libbpp-core-dev (>= 2.3.1)
Section: libdevel
Priority: optional
Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Description: Bio++ Sequence 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 Bio++
classes for sequence analysis classes.
drwxr-xr-x root/root 0 2017-08-23 17:38 ./
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/include/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/include/Bpp/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/include/Bpp/Seq/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/include/Bpp/Seq/Alphabet/
-rw-r--r-- root/root 9381 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h
-rw-r--r-- root/root 17538 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/Alphabet.h
-rw-r--r-- root/root 6291 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/AlphabetExceptions.h
-rw-r--r-- root/root 2835 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/AlphabetNumericState.h
-rw-r--r-- root/root 3834 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/AlphabetState.h
-rw-r--r-- root/root 8370 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/AlphabetTools.h
-rw-r--r-- root/root 2956 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/BinaryAlphabet.h
-rw-r--r-- root/root 4567 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h
-rw-r--r-- root/root 6350 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/CodonAlphabet.h
-rw-r--r-- root/root 3181 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/DNA.h
-rw-r--r-- root/root 3102 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/DefaultAlphabet.h
-rw-r--r-- root/root 2984 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/IntegerAlphabet.h
-rw-r--r-- root/root 4206 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h
-rw-r--r-- root/root 3307 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/LexicalAlphabet.h
-rw-r--r-- root/root 8931 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h
-rw-r--r-- root/root 4181 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/NucleicAlphabetState.h
-rw-r--r-- root/root 3962 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/NumericAlphabet.h
-rw-r--r-- root/root 4912 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/ProteicAlphabet.h
-rw-r--r-- root/root 2784 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/ProteicAlphabetState.h
-rw-r--r-- root/root 3130 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/RNA.h
-rw-r--r-- root/root 4284 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/RNY.h
-rw-r--r-- root/root 11454 2017-06-07 16:40 ./usr/include/Bpp/Seq/Alphabet/WordAlphabet.h
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/include/Bpp/Seq/AlphabetIndex/
-rw-r--r-- root/root 5112 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AAChargeIndex.h
-rw-r--r-- root/root 4349 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h
-rw-r--r-- root/root 3698 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h
-rw-r--r-- root/root 3696 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h
-rw-r--r-- root/root 3619 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h
-rw-r--r-- root/root 3340 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h
-rw-r--r-- root/root 3982 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h
-rw-r--r-- root/root 3533 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AAMassIndex.h
-rw-r--r-- root/root 3698 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AASEA1030Index.h
-rw-r--r-- root/root 3725 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h
-rw-r--r-- root/root 3724 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AASEASup30Index.h
-rw-r--r-- root/root 3593 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h
-rw-r--r-- root/root 3562 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h
-rw-r--r-- root/root 3083 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h
-rw-r--r-- root/root 3416 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h
-rw-r--r-- root/root 3275 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/BLOSUM50.h
-rw-r--r-- root/root 3610 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h
-rw-r--r-- root/root 5580 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h
-rw-r--r-- root/root 4184 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h
-rw-r--r-- root/root 4145 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h
-rw-r--r-- root/root 4137 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h
-rw-r--r-- root/root 3730 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h
-rw-r--r-- root/root 4238 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h
-rw-r--r-- root/root 3341 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/SimpleScore.h
-rw-r--r-- root/root 3212 2017-06-07 16:40 ./usr/include/Bpp/Seq/AlphabetIndex/UserAlphabetIndex1.h
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/include/Bpp/Seq/App/
-rw-r--r-- root/root 12419 2017-06-07 16:40 ./usr/include/Bpp/Seq/App/SequenceApplicationTools.h
-rw-r--r-- root/root 11039 2017-06-07 16:40 ./usr/include/Bpp/Seq/CodonSiteTools.h
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/include/Bpp/Seq/Container/
-rw-r--r-- root/root 5206 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/AbstractSequenceContainer.h
-rw-r--r-- root/root 7470 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/AlignedSequenceContainer.h
-rw-r--r-- root/root 12860 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/CompressedVectorSiteContainer.h
-rw-r--r-- root/root 8707 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/MapSequenceContainer.h
-rw-r--r-- root/root 9485 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/OrderedSequenceContainer.h
-rw-r--r-- root/root 11413 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/SequenceContainer.h
-rw-r--r-- root/root 4361 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/SequenceContainerExceptions.h
-rw-r--r-- root/root 3137 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/SequenceContainerIterator.h
-rw-r--r-- root/root 13016 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/SequenceContainerTools.h
-rw-r--r-- root/root 6991 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/SiteContainer.h
-rw-r--r-- root/root 2944 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/SiteContainerExceptions.h
-rw-r--r-- root/root 3884 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/SiteContainerIterator.h
-rw-r--r-- root/root 23703 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/SiteContainerTools.h
-rw-r--r-- root/root 10412 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/VectorSequenceContainer.h
-rw-r--r-- root/root 10295 2017-06-07 16:40 ./usr/include/Bpp/Seq/Container/VectorSiteContainer.h
-rw-r--r-- root/root 6403 2017-06-07 16:40 ./usr/include/Bpp/Seq/CoreSequence.h
-rw-r--r-- root/root 4280 2017-06-07 16:40 ./usr/include/Bpp/Seq/CoreSite.h
-rw-r--r-- root/root 3378 2017-06-07 16:40 ./usr/include/Bpp/Seq/DNAToRNA.h
-rw-r--r-- root/root 7414 2017-06-07 16:40 ./usr/include/Bpp/Seq/DistanceMatrix.h
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/include/Bpp/Seq/GeneticCode/
-rw-r--r-- root/root 3710 2017-06-07 16:40 ./usr/include/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h
-rw-r--r-- root/root 3581 2017-06-07 16:40 ./usr/include/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h
-rw-r--r-- root/root 8395 2017-06-07 16:40 ./usr/include/Bpp/Seq/GeneticCode/GeneticCode.h
-rw-r--r-- root/root 3697 2017-06-07 16:40 ./usr/include/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h
-rw-r--r-- root/root 3727 2017-06-07 16:40 ./usr/include/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h
-rw-r--r-- root/root 3525 2017-06-07 16:40 ./usr/include/Bpp/Seq/GeneticCode/StandardGeneticCode.h
-rw-r--r-- root/root 3784 2017-06-07 16:40 ./usr/include/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h
-rw-r--r-- root/root 3539 2017-06-07 16:40 ./usr/include/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/include/Bpp/Seq/Io/
-rw-r--r-- root/root 5562 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/AbstractIAlignment.h
-rw-r--r-- root/root 5496 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/AbstractISequence.h
-rw-r--r-- root/root 2667 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/AbstractOAlignment.h
-rw-r--r-- root/root 3465 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/AbstractOSequence.h
-rw-r--r-- root/root 3340 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/BppOAlignmentReaderFormat.h
-rw-r--r-- root/root 3350 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/BppOAlignmentWriterFormat.h
-rw-r--r-- root/root 3968 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/BppOAlphabetIndex1Format.h
-rw-r--r-- root/root 3968 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/BppOAlphabetIndex2Format.h
-rw-r--r-- root/root 3329 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/BppOSequenceReaderFormat.h
-rw-r--r-- root/root 3357 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h
-rw-r--r-- root/root 3331 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/BppOSequenceWriterFormat.h
-rw-r--r-- root/root 4860 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/Clustal.h
-rw-r--r-- root/root 3306 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/Dcse.h
-rw-r--r-- root/root 7593 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/Fasta.h
-rw-r--r-- root/root 2716 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/GenBank.h
-rw-r--r-- root/root 4331 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/ISequence.h
-rw-r--r-- root/root 2594 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/ISequenceStream.h
-rw-r--r-- root/root 2156 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/IoSequence.h
-rw-r--r-- root/root 4364 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/IoSequenceFactory.h
-rw-r--r-- root/root 2057 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/IoSequenceStream.h
-rw-r--r-- root/root 8650 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/Mase.h
-rw-r--r-- root/root 6002 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/MaseTools.h
-rw-r--r-- root/root 4795 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/NexusIoSequence.h
-rw-r--r-- root/root 2981 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/NexusTools.h
-rw-r--r-- root/root 4356 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/OSequence.h
-rw-r--r-- root/root 2499 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/OSequenceStream.h
-rw-r--r-- root/root 4909 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/PhredPhd.h
-rw-r--r-- root/root 2936 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/PhredPoly.h
-rw-r--r-- root/root 6835 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/Phylip.h
-rw-r--r-- root/root 2625 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/SequenceFileIndex.h
-rw-r--r-- root/root 3788 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/Stockholm.h
-rw-r--r-- root/root 4174 2017-06-07 16:40 ./usr/include/Bpp/Seq/Io/StreamSequenceIterator.h
-rw-r--r-- root/root 3717 2017-06-07 16:40 ./usr/include/Bpp/Seq/NucleicAcidsReplication.h
-rw-r--r-- root/root 11621 2017-06-07 16:40 ./usr/include/Bpp/Seq/Sequence.h
-rw-r--r-- root/root 4598 2017-06-07 16:40 ./usr/include/Bpp/Seq/SequenceExceptions.h
-rw-r--r-- root/root 3171 2017-06-07 16:40 ./usr/include/Bpp/Seq/SequenceIterator.h
-rw-r--r-- root/root 6708 2017-06-07 16:40 ./usr/include/Bpp/Seq/SequencePositionIterators.h
-rw-r--r-- root/root 17072 2017-06-07 16:40 ./usr/include/Bpp/Seq/SequenceTools.h
-rw-r--r-- root/root 2926 2017-06-07 16:40 ./usr/include/Bpp/Seq/SequenceWalker.h
-rw-r--r-- root/root 14837 2017-06-07 16:40 ./usr/include/Bpp/Seq/SequenceWithAnnotation.h
-rw-r--r-- root/root 7094 2017-06-07 16:40 ./usr/include/Bpp/Seq/SequenceWithAnnotationTools.h
-rw-r--r-- root/root 26451 2017-06-07 16:40 ./usr/include/Bpp/Seq/SequenceWithQuality.h
-rw-r--r-- root/root 7347 2017-06-07 16:40 ./usr/include/Bpp/Seq/SequenceWithQualityTools.h
-rw-r--r-- root/root 5848 2017-06-07 16:40 ./usr/include/Bpp/Seq/Site.h
-rw-r--r-- root/root 3355 2017-06-07 16:40 ./usr/include/Bpp/Seq/SiteExceptions.h
-rw-r--r-- root/root 2354 2017-06-07 16:40 ./usr/include/Bpp/Seq/SiteIterator.h
-rw-r--r-- root/root 8688 2017-06-07 16:40 ./usr/include/Bpp/Seq/SiteTools.h
-rw-r--r-- root/root 7669 2017-06-07 16:40 ./usr/include/Bpp/Seq/StringSequenceTools.h
-rw-r--r-- root/root 22644 2017-06-07 16:40 ./usr/include/Bpp/Seq/SymbolList.h
-rw-r--r-- root/root 8342 2017-06-07 16:40 ./usr/include/Bpp/Seq/SymbolListTools.h
-rw-r--r-- root/root 5580 2017-06-07 16:40 ./usr/include/Bpp/Seq/Transliterator.h
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/lib/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/cmake/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/cmake/bpp-seq/
-rw-r--r-- root/root 1610 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/cmake/bpp-seq/bpp-seq-config-version.cmake
-rw-r--r-- root/root 2261 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/cmake/bpp-seq/bpp-seq-config.cmake
-rw-r--r-- root/root 1470 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/cmake/bpp-seq/bpp-seq-targets-none.cmake
-rw-r--r-- root/root 3928 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/cmake/bpp-seq/bpp-seq-targets.cmake
-rw-r--r-- root/root 5641808 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/libbpp-seq.a
lrwxrwxrwx root/root 0 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/libbpp-seq.so -> libbpp-seq.so.11
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/share/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/share/doc/libbpp-seq-dev/
-rw-r--r-- root/root 1475 2017-08-23 17:38 ./usr/share/doc/libbpp-seq-dev/changelog.Debian.gz
-rw-r--r-- root/root 5033 2017-06-07 16:40 ./usr/share/doc/libbpp-seq-dev/changelog.gz
-rw-r--r-- root/root 3115 2017-08-23 17:38 ./usr/share/doc/libbpp-seq-dev/copyright
libbpp-seq11-dbgsym_2.3.1-8_armhf.deb
-------------------------------------
new debian package, version 2.0.
size 7486194 bytes: control archive=473 bytes.
403 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libbpp-seq11-dbgsym
Source: libbpp-seq
Version: 2.3.1-8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7727
Depends: libbpp-seq11 (= 2.3.1-8)
Section: debug
Priority: extra
Multi-Arch: same
Description: Debug symbols for libbpp-seq11
Build-Ids: 96fbff74886285606835daea46bfe84b51f89b8f
drwxr-xr-x root/root 0 2017-08-23 17:38 ./
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/lib/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/lib/debug/.build-id/96/
-rw-r--r-- root/root 7901992 2017-08-23 17:38 ./usr/lib/debug/.build-id/96/fbff74886285606835daea46bfe84b51f89b8f.debug
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/share/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-08-23 17:38 ./usr/share/doc/libbpp-seq11-dbgsym -> libbpp-seq11
libbpp-seq11_2.3.1-8_armhf.deb
------------------------------
new debian package, version 2.0.
size 404716 bytes: control archive=932 bytes.
841 bytes, 19 lines control
309 bytes, 4 lines md5sums
27 bytes, 1 lines shlibs
67 bytes, 2 lines triggers
Package: libbpp-seq11
Source: libbpp-seq
Version: 2.3.1-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1752
Depends: libbpp-core3 (>= 2.3.1), libc6 (>= 2.23), 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++ Sequence 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 sequence analysis.
drwxr-xr-x root/root 0 2017-08-23 17:38 ./
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/lib/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11 -> libbpp-seq.so.11.0.0
-rw-r--r-- root/root 1770916 2017-08-23 17:38 ./usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/share/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-08-23 17:38 ./usr/share/doc/libbpp-seq11/
-rw-r--r-- root/root 1475 2017-08-23 17:38 ./usr/share/doc/libbpp-seq11/changelog.Debian.gz
-rw-r--r-- root/root 5033 2017-06-07 16:40 ./usr/share/doc/libbpp-seq11/changelog.gz
-rw-r--r-- root/root 3115 2017-08-23 17:38 ./usr/share/doc/libbpp-seq11/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 203624
Build-Time: 532
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 150
Job: libbpp-seq_2.3.1-8
Machine Architecture: armhf
Package: libbpp-seq
Package-Time: 699
Source-Version: 2.3.1-8
Space: 203624
Status: successful
Version: 2.3.1-8
--------------------------------------------------------------------------------
Finished at 2017-08-29T05:34:08Z
Build needed 00:11:39, 203624k disk space